Diff of the two buildlogs: -- --- b1/build.log 2021-05-21 19:00:08.419257392 +0000 +++ b2/build.log 2021-05-21 19:21:05.658114273 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri May 21 05:40:49 -12 2021 -I: pbuilder-time-stamp: 1621618849 +I: Current time: Fri Jun 24 15:23:15 +14 2022 +I: pbuilder-time-stamp: 1656033795 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -17,8 +17,8 @@ I: copying [./seqan2_2.4.0+dfsg-14.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.igaOGWIF/trustedkeys.kbx': General error -gpgv: Signature made Sat Feb 13 17:44:42 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.O7SgQ2Cb/trustedkeys.kbx': General error +gpgv: Signature made Sun Feb 14 19:44:42 2021 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tillea@rki.de" gpgv: Can't check signature: No public key @@ -40,137 +40,171 @@ dpkg-source: info: applying python3 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22033/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-i386. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=10' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=18' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='a62f969372204acdbda1b05c0f7fd0b8' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='22033' - PS1='# ' - PS2='> ' + INVOCATION_ID=06873b50b0c047b7a01ea9b135ee1869 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=22548 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.oWRKR932Lq/pbuilderrc_Eb8m --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.oWRKR932Lq/b1 --logfile b1/build.log seqan2_2.4.0+dfsg-14.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://78.137.99.97:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.oWRKR932Lq/pbuilderrc_WdgM --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.oWRKR932Lq/b2 --logfile b2/build.log --extrapackages usrmerge seqan2_2.4.0+dfsg-14.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://85.184.249.68:3128 I: uname -a - Linux ionos12-i386 4.19.0-16-686-pae #1 SMP Debian 4.19.181-1 (2021-03-19) i686 GNU/Linux + Linux i-capture-the-hostname 4.19.0-16-amd64 #1 SMP Debian 4.19.181-1 (2021-03-19) x86_64 GNU/Linux I: ls -l /bin - total 5796 - -rwxr-xr-x 1 root root 1367848 Feb 24 08:57 bash - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 38280 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 17768 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 38824 Sep 22 2020 cat - -rwxr-xr-x 1 root root 71624 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 67528 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 75752 Sep 22 2020 chown - -rwxr-xr-x 1 root root 157960 Sep 22 2020 cp - -rwxr-xr-x 1 root root 128724 Dec 10 01:23 dash - -rwxr-xr-x 1 root root 124904 Sep 22 2020 date - -rwxr-xr-x 1 root root 92172 Sep 22 2020 dd - -rwxr-xr-x 1 root root 100752 Sep 22 2020 df - -rwxr-xr-x 1 root root 153964 Sep 22 2020 dir - -rwxr-xr-x 1 root root 83644 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 34664 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 34664 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 71928 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 30112 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 210488 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 100952 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 21916 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 83980 Sep 22 2020 ln - -rwxr-xr-x 1 root root 55572 Feb 7 2020 login - -rwxr-xr-x 1 root root 153964 Sep 22 2020 ls - -rwxr-xr-x 1 root root 153124 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 96328 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 79912 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 47048 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 58920 Feb 7 02:38 more - -rwsr-xr-x 1 root root 50720 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 13856 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 157996 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 38824 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Feb 24 08:57 rbash -> bash - -rwxr-xr-x 1 root root 46984 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 75720 Sep 22 2020 rm - -rwxr-xr-x 1 root root 46984 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 22292 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 125036 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 May 19 21:26 sh -> dash - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 83880 Sep 22 2020 stty - -rwsr-xr-x 1 root root 79396 Feb 7 02:38 su - -rwxr-xr-x 1 root root 34696 Sep 22 2020 sync - -rwxr-xr-x 1 root root 602584 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 13860 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 108520 Sep 22 2020 touch - -rwxr-xr-x 1 root root 34664 Sep 22 2020 true - -rwxr-xr-x 1 root root 17768 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 30236 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 34664 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 153964 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 63024 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/22033/tmp/hooks/D02_print_environment finished + total 5776 + -rwxr-xr-x 1 root root 1367848 Feb 25 2021 bash + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 38280 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 17768 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 38824 Sep 23 2020 cat + -rwxr-xr-x 1 root root 71624 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 67528 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 75752 Sep 23 2020 chown + -rwxr-xr-x 1 root root 157960 Sep 23 2020 cp + -rwxr-xr-x 1 root root 128724 Dec 11 2020 dash + -rwxr-xr-x 1 root root 124904 Sep 23 2020 date + -rwxr-xr-x 1 root root 92172 Sep 23 2020 dd + -rwxr-xr-x 1 root root 100752 Sep 23 2020 df + -rwxr-xr-x 1 root root 153964 Sep 23 2020 dir + -rwxr-xr-x 1 root root 83644 Feb 8 2021 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 34664 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 34664 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 71928 Feb 8 2021 findmnt + -rwsr-xr-x 1 root root 30112 Feb 27 2021 fusermount + -rwxr-xr-x 1 root root 210488 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 2021 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 2021 gzexe + -rwxr-xr-x 1 root root 100952 Mar 3 2021 gzip + -rwxr-xr-x 1 root root 21916 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 83980 Sep 23 2020 ln + -rwxr-xr-x 1 root root 55572 Feb 8 2020 login + -rwxr-xr-x 1 root root 153964 Sep 23 2020 ls + -rwxr-xr-x 1 root root 153124 Feb 8 2021 lsblk + -rwxr-xr-x 1 root root 96328 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 79912 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 47048 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 58920 Feb 8 2021 more + -rwsr-xr-x 1 root root 50720 Feb 8 2021 mount + -rwxr-xr-x 1 root root 13856 Feb 8 2021 mountpoint + -rwxr-xr-x 1 root root 157996 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 2021 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 38824 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Feb 25 2021 rbash -> bash + -rwxr-xr-x 1 root root 46984 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 75720 Sep 23 2020 rm + -rwxr-xr-x 1 root root 46984 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 22292 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 125036 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jun 24 15:23 sh -> bash + lrwxrwxrwx 1 root root 4 Jun 24 05:46 sh.distrib -> dash + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 83880 Sep 23 2020 stty + -rwsr-xr-x 1 root root 79396 Feb 8 2021 su + -rwxr-xr-x 1 root root 34696 Sep 23 2020 sync + -rwxr-xr-x 1 root root 602584 Feb 17 2021 tar + -rwxr-xr-x 1 root root 13860 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 108520 Sep 23 2020 touch + -rwxr-xr-x 1 root root 34664 Sep 23 2020 true + -rwxr-xr-x 1 root root 17768 Feb 27 2021 ulockmgr_server + -rwsr-xr-x 1 root root 30236 Feb 8 2021 umount + -rwxr-xr-x 1 root root 34664 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 2021 uncompress + -rwxr-xr-x 1 root root 153964 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 63024 Feb 8 2021 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 2021 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 2021 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 2021 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 2021 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 2021 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 2021 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 2021 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 2021 zless + -rwxr-xr-x 1 root root 1842 Mar 3 2021 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 2021 znew +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -298,7 +332,7 @@ Get: 74 http://deb.debian.org/debian bullseye/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 75 http://deb.debian.org/debian bullseye/main i386 libbz2-dev i386 1.0.8-4 [31.3 kB] Get: 76 http://deb.debian.org/debian bullseye/main i386 zlib1g-dev i386 1:1.2.11.dfsg-2 [194 kB] -Fetched 47.6 MB in 9s (5249 kB/s) +Fetched 47.6 MB in 1s (74.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19674 files and directories currently installed.) @@ -621,8 +655,44 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main i386 libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main i386 libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main i386 libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main i386 usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 0s (4757 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 41293 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/seqan2-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b +I: Running cd /build/seqan2-2.4.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package seqan2 dpkg-buildpackage: info: source version 2.4.0+dfsg-14 dpkg-buildpackage: info: source distribution unstable @@ -1125,7 +1195,7 @@ debian/rules override_dh_auto_build-arch make[1]: Entering directory '/build/seqan2-2.4.0+dfsg' dh_auto_build --arch "" - cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/seqan2-2.4.0+dfsg -B/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -1135,123 +1205,211 @@ make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/DependInfo.cmake --color= -make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/depend.internal". +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/depend.internal". -Scanning dependencies of target seqan_library Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend.internal". 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Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend.internal". 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depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend.internal". +Dependee 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/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend.internal". +Scanning dependencies of target pair_align_global_1101 +Scanning dependencies of target pair_align_global_1010 +Scanning dependencies of target pair_align_global_0101 +Scanning dependencies of target pair_align_lcs +Scanning dependencies of target pair_align_global_1001 +Scanning dependencies of target pair_align_global_1100 +Scanning dependencies of target pair_align_global_0011 Scanning dependencies of target pair_align_global_0001 +Scanning dependencies of target pair_align_global_1110 +Scanning dependencies of target pair_align_global_1111 +Scanning dependencies of target pair_align_global_0100 +Scanning dependencies of target pair_align_local +Scanning dependencies of target pair_align_global_1011 +Scanning dependencies of target pair_align_global_0010 +Scanning dependencies of target pair_align_global_0110 +Scanning dependencies of target pair_align_global_0000 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build -Scanning dependencies of target pair_align_global_1111 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target pair_align_global_0110 -Scanning dependencies of target pair_align_global_1100 -Scanning dependencies of target pair_align_global_1001 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target pair_align_local -Scanning dependencies of target pair_align_lcs make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f 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'/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build -make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o +[ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 0%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o [ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 1%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o +[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o +[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp Scanning dependencies of target mason_sim +Scanning dependencies of target pair_align_global_0111 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o +[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 2%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/external_split_merge.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/external_split_merge.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, @@ -1282,35 +1440,6 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.h:52, from /build/seqan2-2.4.0+dfsg/apps/mason2/external_split_merge.cpp:35: @@ -1396,10 +1525,9 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -1410,14 +1538,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -1427,9 +1555,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -1509,21 +1636,49 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -1532,6 +1687,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -1561,29 +1723,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -1706,16 +1874,11 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -1740,9 +1903,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -1770,17 +1932,11 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -1799,21 +1955,50 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -1822,6 +2007,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -1857,7 +2049,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -1871,14 +2063,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -1947,7 +2139,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -1961,14 +2153,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -1978,17 +2170,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2011,7 +2198,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -2026,25 +2213,25 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2053,6 +2240,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2081,17 +2275,13 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2099,32 +2289,32 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2133,6 +2323,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2192,17 +2389,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2227,16 +2419,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2261,16 +2449,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2312,25 +2496,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2339,67 +2519,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2408,65 +2565,64 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2490,18 +2646,13 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2509,36 +2660,32 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2547,33 +2694,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2582,32 +2717,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2616,68 +2740,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2686,30 +2786,18 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2728,26 +2816,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -2756,29 +2839,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -2798,50 +2896,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' @@ -2873,18 +2958,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -2892,14 +2976,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -2909,16 +2993,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -2978,16 +3061,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3012,18 +3094,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3031,14 +3112,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -3047,18 +3128,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3066,14 +3146,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -3083,9 +3163,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' @@ -3118,16 +3197,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3153,16 +3232,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3188,9 +3266,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' @@ -3223,16 +3300,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3257,18 +3333,18 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3276,14 +3352,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -3293,16 +3369,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3328,16 +3403,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3363,16 +3438,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3398,16 +3473,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3433,16 +3508,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3468,16 +3542,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3503,16 +3577,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3538,16 +3612,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3572,18 +3645,18 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3591,14 +3664,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -3608,16 +3681,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3637,90 +3710,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 2%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = GenomicInterval]': -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]' -/build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:718:51: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1441 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1453 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1475 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -3728,81 +3748,54 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Built target pair_align_lcs -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend.internal". -Scanning dependencies of target pair_align_global_1010 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -[ 2%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3827,12 +3820,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -3851,44 +3848,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3920,10 +3895,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3955,10 +3930,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -3983,18 +3958,18 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4002,111 +3977,25 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' @@ -4134,30 +4023,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Built target pair_align_global_1100 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend.internal". -Scanning dependencies of target pair_align_global_0010 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4176,33 +4058,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Built target pair_align_global_1001 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend.internal". -Scanning dependencies of target pair_align_global_0011 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -[ 2%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4221,45 +4093,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4267,14 +4117,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -4284,16 +4134,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4325,10 +4175,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4354,16 +4204,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4389,16 +4239,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4418,47 +4268,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 2%] Built target pair_align_global_0110 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend.internal". -Scanning dependencies of target pair_align_global_1101 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1110 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4477,24 +4303,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target pair_align_global_0100 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4513,57 +4338,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0001 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend.internal". -Scanning dependencies of target pair_align_global_0101 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4595,10 +4385,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4618,17 +4408,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1111 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend.internal". -Scanning dependencies of target pair_align_global_1011 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -4641,10 +4420,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4664,92 +4443,57 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0000 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4769,44 +4513,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target pair_align_global_0111 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=1 -DSUFFIX_GAP_LEFT=1 -DSUFFIX_GAP_RIGHT=1 -DSUFFIX_GAP_TOP=0 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4814,14 +4537,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -4831,16 +4554,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4866,12 +4589,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4890,45 +4618,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -4936,14 +4642,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -4953,16 +4659,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -4994,10 +4700,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5023,16 +4729,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5057,18 +4763,18 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:41:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5076,14 +4782,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lcs.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -5093,11 +4799,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5122,11 +4834,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5151,12 +4869,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5181,12 +4904,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5205,21 +4933,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -5228,44 +4961,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5291,15 +5009,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5325,16 +5044,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5360,16 +5079,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5394,18 +5113,18 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::Tag; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::Tag; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:41:70: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5413,14 +5132,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_local.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -5430,16 +5149,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5471,10 +5190,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5500,11 +5219,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5529,11 +5254,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5558,16 +5289,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5593,12 +5324,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5658,12 +5394,17 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig<>; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig<>; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig<>]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -5682,21 +5423,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -5705,46 +5451,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5776,10 +5505,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5805,16 +5534,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5840,15 +5569,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5874,16 +5604,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5909,16 +5639,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5944,16 +5674,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -5979,16 +5709,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -6008,35 +5738,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_local -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend.internal". -Scanning dependencies of target pair_align_global_1000 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -6068,10 +5785,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -6103,10 +5820,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:86:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:184:19: required from 'void pairwise_align(const TScore&, TSeqFile&, TMethod, TDiag, TDiag, bool, TOutfile&) [with TAlphabet = seqan::SimpleType; TAlignConfig = seqan::AlignConfig; TScore = seqan::Score, seqan::Tag > >; TSeqFile = std::__cxx11::basic_string; TMethod = seqan::Tag; TDiag = int; TOutfile = std::__cxx11::basic_string]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:276:42: required from 'void _initAlignParams(const Options&, TScore&, const TAlgorithm&, TAlignSpec) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >; TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:289:31: required from 'void _initScoreMatrix(const Options&, seqan::Dna5, const TAlgorithm&, const TAlignSpec&) [with TAlgorithm = seqan::Tag; TAlignSpec = seqan::AlignConfig; seqan::Dna5 = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:364:52: required from 'void pairAlignConfig(const Options&, const TAlgorithm&, const TSpec&) [with TAlgorithm = seqan::Tag; TSpec = seqan::AlignConfig]' /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp:73:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -6126,10 +5843,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/genomic_variants.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -6137,10 +5856,57 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = GenomicInterval]': +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = int; TCargo = GenomicInterval; TValue2 = int]' +/build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:718:51: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1441 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1453 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1475 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -6150,25 +5916,26 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -6179,26 +5946,25 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -6210,13 +5976,28 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_lcs +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend.internal". +Scanning dependencies of target pair_align_global_1000 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -DSUFFIX_GAP_BOTTOM=0 -DSUFFIX_GAP_LEFT=0 -DSUFFIX_GAP_RIGHT=0 -DSUFFIX_GAP_TOP=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_global.cpp +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/mason_options.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/mason_options.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -6300,6 +6081,92 @@ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_options.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, @@ -6473,23 +6340,180 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/methylation_levels.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1100 +make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend.internal". +Scanning dependencies of target test_funcs_param_chooser +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0100 +make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/depend.internal". +Scanning dependencies of target param_chooser +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1110 +make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/depend.internal". +Scanning dependencies of target rabema_do_search +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0000 +make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend.internal". +Scanning dependencies of target rabema_build_gold_standard +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0110 +make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend.internal". +Scanning dependencies of target rabema_evaluate +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1101 +make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend.internal". +Scanning dependencies of target rabema_prepare_sam +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0101 +make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/depend.internal". +Scanning dependencies of target razers +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1010 +make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend.internal". +Scanning dependencies of target razers3_quality2prob +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:44: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1001 +make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend.internal". +Scanning dependencies of target razers3_simulate_reads +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -6499,25 +6523,52 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0001 +make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1111 +make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -6528,26 +6579,37 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target rep_sep +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target razers3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build +[ 3%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -6559,67 +6621,25 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1010 -make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend +[ 3%] Built target pair_align_global_0010 +make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend.internal". -Scanning dependencies of target test_funcs_param_chooser +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/depend.internal". +Scanning dependencies of target sak make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build +make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 3%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sak.dir/sak.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: @@ -6757,6 +6777,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/test_param_chooser.cpp:47: @@ -6805,10 +6839,82 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1011 +make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +Scanning dependencies of target sam2matrix +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:79: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:118: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -6818,54 +6924,22 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -6873,224 +6947,95 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_0111 +make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:26: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp -[ 3%] Linking CXX executable ../../bin/test_funcs_param_chooser -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target test_funcs_param_chooser -make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/depend.internal". -Scanning dependencies of target param_chooser +Scanning dependencies of target samcat make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build +make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/param_chooser/CMakeFiles/param_chooser.dir/param_chooser.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/param_chooser.dir/param_chooser.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 141 | _cargo() - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +[ 3%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/samcat.dir/samcat.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:604:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:64: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: @@ -7137,26 +7082,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 625 | return ModifiedString(host); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -7175,34 +7127,6 @@ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': @@ -7225,6 +7149,52 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: @@ -7248,19 +7218,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h: In instantiation of 'bool seqan::matchVerify(TMatch&, seqan::Segment, unsigned int, TReadSet&, TMyersPatterns&, const seqan::RazerSOptions&, seqan::SwiftSemiGlobal) [with TMatch = seqan::ReadMatch; TGenome = seqan::String, seqan::Alloc<> >; TReadSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TMyersPatterns = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >, seqan::Alloc<> >; TSpec = seqan::RazerSSpec; seqan::SwiftSemiGlobal = seqan::Tag >]': @@ -7285,22 +7242,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:32, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:39: @@ -7324,58 +7265,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:64: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' + 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, @@ -7401,6 +7325,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/../splazers/paramChooser.h:34, @@ -7425,6 +7350,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ +[ 3%] Built target pair_align_global_0011 +make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -7535,6 +7466,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ +Scanning dependencies of target s4_join +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_join.dir/join.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/apps/param_chooser/param_chooser.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -7776,53 +7713,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0010 -make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/depend.internal". -Scanning dependencies of target rabema_do_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_do_search.dir/do_search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_do_search.dir/do_search.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' @@ -7831,20 +7726,25 @@ 478 | return TIterator(me, end(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' @@ -7853,28 +7753,23 @@ 343 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1101 -make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -7884,27 +7779,113 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target rabema_build_gold_standard +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build +[ 3%] Built target pair_align_local +make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/depend.internal". +Scanning dependencies of target s4_search +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_search.dir/search.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -7915,20 +7896,23 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -7940,14 +7924,17 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' @@ -7956,223 +7943,323 @@ /build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' /build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 625 | return ModifiedString(host); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:7: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' /build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' /build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:27:89: required from here +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/apps/rabema/do_search.cpp:8: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0100 -make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake --color= -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/depend.internal". -[ 3%] Built target pair_align_global_0011 -make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake --color= -Scanning dependencies of target rabema_evaluate -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend.internal". -make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp -Scanning dependencies of target rabema_prepare_sam -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/rabema/CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:72:7: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:644:22: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1441 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1453 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1475 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:254:100: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_454.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_454.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, + from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 141 | _cargo() - | ^ + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 625 | return ModifiedString(host); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 150 | ModifiedString(typename Parameter_::Type host): + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0101 -make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:64: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target razers -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/razers/CMakeFiles/razers.dir/razers.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -8183,106 +8270,197 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:79: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:513:97: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::InfixSegment>; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/curve_smoothing.h:257:118: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::InfixSegment>; TIterator = WeightedMatch*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -8295,7 +8473,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -8303,46 +8481,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:64: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -8353,7 +8500,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -8361,167 +8508,235 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 625 | return ModifiedString(host); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:403:41: required from 'void buildErrorCurvePoints(seqan::String&, int&, TContigSeq&, size_t, bool, TReadSeq&, size_t, size_t, const TReadNames&, bool, const TPatternSpec&) [with TContigSeq = seqan::String, seqan::Alloc<> >; TReadSeq = seqan::String, seqan::Alloc<> >; TPatternSpec = seqan::Tag; TReadNames = seqan::StringSet > >; size_t = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:899:34: required from 'int matchesToErrorFunction(TErrorCurves&, seqan::String&, seqan::BamFileIn&, seqan::StringSet > >&, const seqan::StringSet > >&, const seqan::FaiIndex&, const BuildGoldStandardOptions&, const TPatternSpec&) [with TPatternSpec = seqan::Tag; TErrorCurves = std::map >; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:1204:105: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_build_gold_standard.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 3%] Linking CXX executable ../../bin/rabema_do_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rabema_do_search -make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend.internal". -Scanning dependencies of target razers3_quality2prob -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -8529,71 +8744,38 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1502:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2) [with TValue = unsigned int; TCargo = unsigned int; TValue2 = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:644:22: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1441 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1453 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1475 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; TSource = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:702:11: required from 'void seqan::assignValue(T&, TPos, const TValue&) [with T = seqan::String, seqan::AlignedReadStoreElement, void>, unsigned int>, seqan::Alloc<> >; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/property_map_generic.h:186:16: required from 'typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = seqan::String, seqan::AlignedReadStoreElement, void>, unsigned int>, seqan::Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; typename seqan::EnableIf >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:191:23: required from 'GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int; typename ReadGraph::TId = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_construction.h:82:59: required from 'void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]' +/build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:217:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph.h:32, + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:34: +/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:44:5: note: because 'GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>' has user-provided 'GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int]' + 44 | GraphCargo(GraphCargo const& other) + | ^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -8607,7 +8789,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -8615,15 +8797,16 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -8632,15 +8815,17 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -8648,7 +8833,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -8663,40 +8848,98 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -8709,149 +8952,346 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/rabema/prepare_sam.cpp:29: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 625 | return ModifiedString(host); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:347:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Myers >; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Myers; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/apps/rabema/find_myers_ukkonen_reads.h:99:24: required from 'seqan::Pattern >::Pattern(TNeedle2&, int) [with TNeedle2 = seqan::String, seqan::Alloc<> >; TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:623:51: required from 'int benchmarkReadResult(RabemaStats&, const seqan::String&, const BamFileIn&, const seqan::String&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, const RefIdMapping&, const RabemaEvaluationOptions&, const TPatternSpec&, bool, bool) [with TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1003:42: required from 'int compareAlignedReadsToReference(RabemaStats&, seqan::BamFileIn&, const seqan::FaiIndex&, const seqan::StringSet, seqan::Alloc<> > >&, TForwardIter&, const RabemaEvaluationOptions&, const TPatternSpec&) [with TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TPatternSpec = seqan::Tag; seqan::BamFileIn = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:1402:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rabema/rabema_evaluate.cpp:28: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, - from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1011 -make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend.internal". -Scanning dependencies of target razers3_simulate_reads -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_0111 -make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/depend.internal". -Scanning dependencies of target razers3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/razers.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: @@ -8881,6 +9321,61 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Linking CXX executable ../../bin/rabema_do_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_do_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_do_search.dir/do_search.cpp.o -o ../../bin/rabema_do_search -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' @@ -8907,6 +9402,119 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target rabema_do_search +make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend.internal". +Scanning dependencies of target seqan_tcoffee +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -8962,19 +9570,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1000 -make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/depend.internal". -Scanning dependencies of target rep_sep -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/rep_sep/CMakeFiles/rep_sep.dir/rep_sep.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/rep_sep.dir/rep_sep.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:319:80: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -8996,6 +9605,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -9101,6 +9720,160 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:332:81: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:357:80: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:370:81: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: @@ -9183,33 +9956,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:49: @@ -9238,33 +10001,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -9297,6 +10051,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:28, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9320,6 +10092,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9341,6 +10138,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9386,6 +10201,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9433,34 +10266,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -9532,6 +10337,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9577,6 +10407,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9601,85 +10449,190 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' 281 | Shape(Shape const &other): | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:28, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9764,6 +10717,83 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.h:28, from /build/seqan2-2.4.0+dfsg/apps/razers/razers.cpp:50: @@ -9788,6 +10818,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -9814,62 +10873,204 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:42:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/quality2prob.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 764 | dbIndex.index = TIndex(db.text); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] + 888 | dbIndex.index[seedSet] = TIndex(db.text); + | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' + 88 | Index(Index const & other) : + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -9894,6 +11095,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -9992,6 +11208,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' @@ -10029,6 +11278,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' @@ -10118,6 +11382,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -10125,6 +11398,480 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -10196,6 +11943,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -10223,6 +12020,190 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:150:17: required from 'void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:98:15: required from 'void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:142:13: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -10251,21 +12232,47 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:740:27: required from 'void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:745:69: required from 'void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -10274,1387 +12281,510 @@ 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +[ 3%] Linking CXX executable ../../bin/test_funcs_param_chooser +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_funcs_param_chooser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_funcs_param_chooser.dir/test_param_chooser.cpp.o -o ../../bin/test_funcs_param_chooser -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target test_funcs_param_chooser +make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +Scanning dependencies of target seqcons2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons.cpp +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 358 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 399 | indexL.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 413 | indexR.shape = shape; + | ~~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 835 | tls.shape = shape; + | ~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 862 | index.shape = shape; + | ~~~~~~~~~~~~^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:120:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/razers3/simulate_reads.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 3%] Linking CXX executable ../../bin/param_chooser -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1348:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1351:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1356:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSPrefix; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1359:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1304:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:75: -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h: In instantiation of 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode, seqan::NMatchesNone_>; seqan::CharString = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1307:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1362:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:672:1: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 672 | SEQAN_OMP_PRAGMA(parallel for private (intBuf) firstprivate(align)) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target param_chooser -make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target sak -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/sak/CMakeFiles/sak.dir/sak.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sak.dir/sak.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; TSource = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:702:11: required from 'void seqan::assignValue(T&, TPos, const TValue&) [with T = seqan::String, seqan::AlignedReadStoreElement, void>, unsigned int>, seqan::Alloc<> >; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/property_map_generic.h:186:16: required from 'typename seqan::EnableIf >, void>::Type seqan::assignProperty(TPropertyMap&, TDescriptor, TValue) [with TPropertyMap = seqan::String, seqan::AlignedReadStoreElement, void>, unsigned int>, seqan::Alloc<> >; TDescriptor = unsigned int; TValue = GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>; typename seqan::EnableIf >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:191:23: required from 'GraphCargo& registerRead(ReadGraph&, typename ReadGraph::TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int; typename ReadGraph::TId = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_construction.h:82:59: required from 'void construct(ReadGraph&, const seqan::String > >&, const seqan::FragmentStore&, TId) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = int]' -/build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:217:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>& GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>::operator=(const GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph.h:32, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:34: -/build/seqan2-2.4.0+dfsg/apps/rep_sep/rgraph_base.h:44:5: note: because 'GraphCargo, seqan::AlignedReadStoreElement, void>, unsigned int>' has user-provided 'GraphCargo::GraphCargo(const GraphCargo&) [with TColumnAlphabet = seqan::Triple; TAlignedReadStoreElement = seqan::AlignedReadStoreElement, void>; TPosition = unsigned int]' - 44 | GraphCargo(GraphCargo const& other) - | ^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/rep_sep/rep_sep.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:740:27: required from 'void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::QualityExtractor >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:745:69: required from 'void seqan::write(TTarget&, seqan::FragmentStore&, Amos) [with TTarget = seqan::VirtualStream >; TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; seqan::Amos = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1222:14: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:785:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1662:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1202:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:358:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 358 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:399:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 399 | indexL.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:413:22: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 413 | indexR.shape = shape; - | ~~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]': -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1197:39: required from 'int seqan::_mapSingleReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:835:19: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 835 | tls.shape = shape; - | ~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:862:21: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 862 | index.shape = shape; - | ~~~~~~~~~~~~^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]': /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesNone_; TFilterSpec = seqan::Pigeonhole]' @@ -11851,6 +12981,58 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_454.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h: In instantiation of 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]': /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' @@ -12415,6 +13597,36 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: @@ -12722,6 +13934,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: @@ -13651,4772 +14894,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; TPosition = int; TCount = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:513:15: required from 'void seqan::insertGap(seqan::Gaps&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps > >; TPosition = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2067:42: required from 'void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TScore = seqan::Score >; TShrinkMatches = seqan::True]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1221:40: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:680:20: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 585 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:941:46: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 577 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:910:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:1006:37: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 577 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 585 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 585 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 585 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:811:66: required from 'void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = seqan::String, seqan::Alloc<> >; TQual = seqan::String >; TRead = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:31: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: required from 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:347:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:11: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:337:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2241:41: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:468:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/tokenization.h:489:23: required from 'void seqan::writeWrappedString(TTarget&, const TSequence&, TSize) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TSequence = seqan::Segment >, seqan::InfixSegment>; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/fasta_fastq.h:475:23: required from 'typename seqan::EnableIf, seqan::Tag > > >, void>::Type seqan::writeRecord(TTarget&, const TIdString&, const TSeqString&, const TQualString&, const Fastq&, const seqan::SequenceOutputOptions&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf, seqan::Tag > > >, void>::Type = void; seqan::Fastq = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:423:16: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::Tag&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TagSpec = seqan::TagFastq_]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:506:20: required from 'void seqan::writeRecord(seqan::FormattedFile, seqan::Tag, TSpec>&, const TIdString&, const TSeqString&, const TQualString&, const seqan::TagSelector&) [with TSpec = void; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/seq_io/sequence_file.h:519:16: required from 'typename seqan::EnableIf >, seqan::IsSequence >, void>::Type seqan::writeRecord(TFile&, const TIdString&, const TSeqString&, const TQualString&) [with TFile = seqan::FormattedFile, seqan::Tag >; TIdString = seqan::String >; TSeqString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TQualString = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::IsSequence >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:424:110: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/sak/sak.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:989:66: required from 'bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1181:44: required from 'bool seqan::_stateInit(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1535:24: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2177:16: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 599 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:24: required from 'void seqan::goEnd(TIterator&) [with TIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:737:10: required from 'void seqan::goEnd(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1537:18: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2245:32: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 278 | TContainer cont(container(host(me))); - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 318 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 318 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' - 143 | Index(Index const &other): - | ^~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 86 | class Index > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 519 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 519 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 318 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 318 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 519 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 519 | class Pattern > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] - 110 | class ThreadLocalStorage< - | ^~~~~~~~~~~~~~~~~~~ - 111 | MapSingleReads< - | ~~~~~~~~~~~~~~~ - 112 | TMatches_, - | ~~~~~~~~~~ - 113 | TFragmentStore, - | ~~~~~~~~~~~~~~~ - 114 | TFilterFinder_, - | ~~~~~~~~~~~~~~~ - 115 | TFilterPattern_, - | ~~~~~~~~~~~~~~~~ - 116 | TShape, - | ~~~~~~~ - 117 | TOptions, - | ~~~~~~~~~ - 118 | TCounts, - | ~~~~~~~~ - 119 | TRazerSMode> > - | ~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' - 281 | Shape(Shape const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:69: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:46: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from 'typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(seqan::Convert >, T>, const seqan::Proxy&) [with THost = seqan::SimpleType; char CHAR = '-'; TSpec = seqan::Tag; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec2 = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >, seqan::Proxy >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:17: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:45: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(const seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:314:32: required from 'typename seqan::Position > >::Type seqan::position(const seqan::ModifiedIterator >&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; typename seqan::Position > >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:675:73: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 288 | TContainer cont(container(host(me))); - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:30: required from 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::SimpleType; TSeqVValue = seqan::SimpleType; TSeqVIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 278 | TContainer cont(container(host(me))); - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 118 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' - 143 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' -/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here -/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 84 | class ThreadLocalStorage > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Linking CXX static library libmason_sim.a -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 -/usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -/usr/bin/ranlib libmason_sim.a -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target mason_sim -make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend.internal". -Scanning dependencies of target sam2matrix -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/sam2matrix/CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:145:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/sam2matrix/sam2matrix.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 3%] Linking CXX executable ../../bin/rabema_prepare_sam -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rabema_prepare_sam -make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/depend.internal". -Scanning dependencies of target samcat -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/samcat/CMakeFiles/samcat.dir/samcat.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/samcat.dir/samcat.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp -[ 3%] Linking CXX executable ../../bin/rabema_build_gold_standard -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz -lbz2 -[ 3%] Linking CXX executable ../../bin/razers3_quality2prob -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rabema_build_gold_standard -make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target razers3_quality2prob -make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/depend.internal". -Scanning dependencies of target s4_join -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target s4_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/searchjoin/CMakeFiles/s4_join.dir/join.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_join.dir/join.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp -[ 3%] Building CXX object apps/searchjoin/CMakeFiles/s4_search.dir/search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/c++ -DSEARCHJOIN_HUGEDB=TRUE -DSEQAN_APP_VERSION=\"0.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/s4_search.dir/search.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/samcat/samcat.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 3%] Linking CXX executable ../../bin/razers3_simulate_reads -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target razers3_simulate_reads -make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend.internal". -Scanning dependencies of target seqan_tcoffee -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.13.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:319:80: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:282:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:323:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:405:10: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = seqan::Tag; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:449:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:332:81: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:357:80: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:355:10: required from 'void index(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:370:81: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void build(DbIndex, TDbIndexSpec>&, Db&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::IndexSa >; TDbIndexSpec = void; TDbSpec = void; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:344:10: required from 'void index(DbFinder&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:264:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:764:19: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 764 | dbIndex.index = TIndex(db.text); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h: In instantiation of 'void buildQuery(DbIndex >, seqan::Tag >&, Db&, TSeedLength) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TDbSpec = void; TSeedLength = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:374:15: required from 'void prepare(DbFinder&, Db&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:279:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:888:32: warning: implicitly-declared 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >& seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >::operator=(const seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >&)' is deprecated [-Wdeprecated-copy] - 888 | dbIndex.index[seedSet] = TIndex(db.text); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag]' - 88 | Index(Index const & other) : - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:50: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:336:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:361:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, void, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:374:88: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder, seqan::Alloc > >, seqan::Owner > >, seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA >& seqan::VertexSA >::operator=(const seqan::VertexSA >&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA >' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, void>; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:197:21: required from 'bool close(Writer >&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:293:10: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:311:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = void; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:791:30: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDbQuerySpec = void; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:349:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag; TSpec = seqan::Truncated; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Truncated]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::StringSet > >, seqan::Owner > >; TTextIndexSpec = seqan::IndexSa >; TPattern = seqan::StringSet > >, seqan::Owner > >; TPatternIndexSpec = seqan::IndexSa >; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = DbFinder > >, seqan::Owner > >, seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >, seqan::Tag, Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:611:14: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>; TSeq2 = seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: required from 'void _writeRecord(Writer&, const TString1&, const TString2&) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; TString1 = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:150:17: required from 'void _write(Writer&, typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:98:15: required from 'void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:142:13: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment > >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter > >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1515:66: required from 'unsigned int seqan::_computeEditDistanceBanded(const TSeq1&, const TSeq2&, unsigned int) [with TSeq1 = seqan::Segment > >, seqan::InfixSegment>; TSeq2 = seqan::Segment > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:136:52: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:536:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment > >, seqan::InfixSegment>::Segment(const seqan::Segment > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 3%] Linking CXX executable ../../bin/rep_sep -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lrt -lz -lbz2 -[ 3%] Linking CXX executable ../../bin/rabema_evaluate -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rep_sep -make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rabema_evaluate -make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/depend.internal". -Scanning dependencies of target seqcons2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build -Scanning dependencies of target sgip -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons.cpp.o -[ 3%] Building CXX object apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sgip.dir/sgip.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sgip/sgip.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -18426,25 +14919,216 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:191:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::Graph >&, FrequencyCounting) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FrequencyCounting = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:178:24: required from 'void seqan::evaluateAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:281:26: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1667 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1679 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1701 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; TPosition = int; TCount = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:513:15: required from 'void seqan::insertGap(seqan::Gaps&, TPosition) [with TSequence = seqan::String, seqan::Alloc<> >; TSpec = seqan::AnchorGaps > >; TPosition = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2067:42: required from 'void seqan::convertMatchesToGlobalAlignment(seqan::FragmentStore&, const TScore&, const TShrinkMatches&) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TScore = seqan::Score >; TShrinkMatches = seqan::True]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1221:40: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:395:32: required from 'seqan::Finder >::Finder(THaystack&, TRepeatSize, TPeriodSize) [with TRepeatSize = int; TPeriodSize = int; THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:680:20: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3247:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 585 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = long unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:941:46: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 577 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:910:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:1006:37: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 577 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 585 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -18466,6 +15150,52 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:932:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:975:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Hamming_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:696:16: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFilterSpec = seqan::Pigeonhole; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::OneGappedShape>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Pigeonhole]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3252:33: required from 'int seqan::_mapMatePairReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 585 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::host(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Swift > >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1866:36: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:2088:30: required from 'bool seqan::windowFindBegin(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1200:29: required from 'void seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, unsigned int, TThreadLocalStorages&, const seqan::String >&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1489:38: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&, TFilterSpec) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_; TFilterSpec = seqan::Swift > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1657:41: required from 'int seqan::_mapMatePairReadsParallel(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const seqan::RazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TScoreMode = seqan::RazerSErrors; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:585:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 585 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': @@ -18494,31 +15224,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -18623,70 +15328,248 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: required from 'void seqan::alignAndGetCigarString(TCigar&, TMDString&, const TContig&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContig = seqan::ContigStoreElement, seqan::Alloc<> >, seqan::GapAnchor, void>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:905:27: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:811:66: required from 'void seqan::_fillBamSeqAndQual(TSeq&, TQual&, const TRead&) [with TSeq = seqan::String, seqan::Alloc<> >; TQual = seqan::String >; TRead = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:936:31: required from 'void seqan::setPrimaryMatch(seqan::BamAlignmentRecord&, seqan::FragmentStore&, const TAlignedRead&, const TAlignQuality&, TBamIOFunctor&, bool) [with TSpec = MyFragStoreConfig; TConfig = seqan::FragmentStoreConfig; TAlignedRead = seqan::AlignedReadStoreElement, void>; TAlignQuality = seqan::AlignQualityStoreElement; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:191:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::Graph >&, FrequencyCounting) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FrequencyCounting = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:178:24: required from 'void seqan::evaluateAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:281:26: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1667 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1679 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1701 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:98:15: required from 'void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:142:13: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: required from 'void seqan::initializeThreadLocalStoragesPaired(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1463:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, @@ -18819,6 +15702,63 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:132:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/searchjoin/writer.h:98:15: required from 'void Writer::operator()(typename seqan::Size::Type, typename seqan::Size::Type) [with TDb = Db, seqan::Alloc > >, seqan::Owner > >, void>; TDbQuery = Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >; TSpec = seqan::Tag; typename seqan::Size::Type = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:142:13: required from 'bool _verify(Verifier&, typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/verifier.h:78:23: required from 'bool Verifier::operator()(typename seqan::Size >::Type, typename seqan::Size >::Type, TDelegate&) [with TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >; TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::Tag; typename seqan::Size >::Type = unsigned int; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:810:30: required from 'void execute(DbFinder, TDelegate, seqan::Tag >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Tag; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:508:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:57: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -18923,39 +15863,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -19060,32 +15967,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -19193,32 +16074,6 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' @@ -19268,58 +16123,112 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:24: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:529:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:507:35: required from 'void seqan::_alignAndGetCigarString(TCigar&, TMDString&, const TContigInfix&, const TReadSeq&, TAlignedRead&, TErrors&, TAlignFunctor&) [with TCigar = seqan::String >; TMDString = seqan::String >; TContigInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TReadSeq = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TAlignedRead = const seqan::AlignedReadStoreElement, void>; TErrors = int; TAlignFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:534:32: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:63: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -19427,6 +16336,32 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' @@ -19476,6 +16411,109 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String, seqan::Alloc > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String, seqan::Alloc > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc > >; TString = seqan::String > >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc > >; TSequence = seqan::String > >; TSetSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -19580,6 +16618,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:469:24: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2241:41: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -19606,12 +16673,236 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1088:24: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::UngappedShape<0> >; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:654:36: required from 'void seqan::_mapMatePairReads(TMatches&, seqan::FragmentStore&, unsigned int, seqan::Pattern&, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:1115:30: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:852:30: required from 'void seqan::initializeThreadLocalStoragesSingle(TThreadLocalStorages&, TFragmentStore&, const TSplitters&, TShape&, TOptions&) [with TThreadLocalStorages = seqan::String, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TSplitters = seqan::String >; TShape = const seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:1008:40: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' @@ -19747,58 +17038,6 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' @@ -19825,6 +17064,32 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' @@ -19926,64 +17191,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' /build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, @@ -20094,58 +17351,6 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = void; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, void>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:286:12: required from 'int runJoiner(Options&, const TText&, const TIndex&, TSpec) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:323:87: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/join.cpp:61: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' @@ -20610,40 +17815,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, @@ -20982,448 +18153,2631 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:32, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:989:66: required from 'bool seqan::_patternInitSmallStateBanded(TFinder&, const TNeedle2&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1181:44: required from 'bool seqan::_stateInit(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1535:24: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::FindInfix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TNeedle2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2177:16: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 599 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:24: required from 'void seqan::goEnd(TIterator&) [with TIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:737:10: required from 'void seqan::goEnd(seqan::Finder&) [with THaystack = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1537:18: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_, seqan::True, TFindBeginPatternSpec> >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::FindPrefix; TFinderCSP = seqan::NMatchesAll_; TPatternCSP = seqan::NMatchesAll_; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1646:16: required from 'bool seqan::find(TFinder&, const TNeedle&, seqan::PatternState_ >&, int) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >, void>; TNeedle = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TNeedle2 = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TSpec = seqan::AlignTextBanded; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2245:32: required from 'bool seqan::matchVerify(TMatchVerifier&, seqan::Segment, unsigned int, const TRead&, const seqan::RazerSMode&) [with TMatchVerifier = seqan::MatchVerifier, seqan::String, seqan::Alloc<> >, seqan::RazerSCoreOptions >, seqan::RazerSMode, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::String > >; TGenome = seqan::String, seqan::Alloc<> >; TRead = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs.h:793:40: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3340:37: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 278 | TContainer cont(container(host(me))); + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = seqan::Pigeonhole; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2795:64: required from 'void seqan::_applyFilterOptions(seqan::Pattern >&, const TOptions&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TPigeonholeSpec = void; TOptions = seqan::RazerSCoreOptions >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3026:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:398:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 318 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:859:24: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 318 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:2948:40: required from 'void seqan::_mapSingleReadsToContig(TMatches&, TFragmentStore&, unsigned int, seqan::Pattern&, TCounts&, char, TRazerSOptions&, const TRazerSMode&) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TReadIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TFilterSpec = seqan::Swift > >; TCounts = seqan::String >; TRazerSOptions = seqan::RazerSCoreOptions >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3054:36: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3343:31: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' + 143 | Index(Index const &other): + | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:86:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 86 | class Index > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 519 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 519 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 318 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 318 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >&)' first required here + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 519 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 519 | class Pattern > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: note: synthesized method 'seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >& seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >::operator=(const seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >&)' first required here + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >; TShape = seqan::Shape, seqan::OneGappedShape>; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: required from 'bool seqan::processRead(seqan::PairedMatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:962:32: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinderL = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterFinderR = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:1314:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:33, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_match_filter.h:251:20: required from 'bool seqan::processRead(seqan::MatchFilter&, unsigned int) [with TOptionsSpec = seqan::RazerSSpec<>; TReadSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TCallback = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:466:36: required from 'void seqan::writeBackToLocal(seqan::ThreadLocalStorage >&, seqan::String >&, bool) [with TMatches = seqan::String, seqan::Alloc<> >; TFragmentStore = seqan::FragmentStore; TFilterFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TFilterPattern = seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >; TShape = seqan::Shape, seqan::GappedShape > >; TOptions = seqan::RazerSCoreOptions >; TCounts = seqan::String >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:769:29: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_parallel.h:110:7: warning: implicitly-declared 'seqan::Shape, seqan::GappedShape > >& seqan::Shape, seqan::GappedShape > >::operator=(const seqan::Shape, seqan::GappedShape > >&)' is deprecated [-Wdeprecated-copy] + 110 | class ThreadLocalStorage< + | ^~~~~~~~~~~~~~~~~~~ + 111 | MapSingleReads< + | ~~~~~~~~~~~~~~~ + 112 | TMatches_, + | ~~~~~~~~~~ + 113 | TFragmentStore, + | ~~~~~~~~~~~~~~~ + 114 | TFilterFinder_, + | ~~~~~~~~~~~~~~~ + 115 | TFilterPattern_, + | ~~~~~~~~~~~~~~~~ + 116 | TShape, + | ~~~~~~~ + 117 | TOptions, + | ~~~~~~~~~ + 118 | TCounts, + | ~~~~~~~~ + 119 | TRazerSMode> > + | ~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_gapped.h:281:9: note: because 'seqan::Shape, seqan::GappedShape > >' has user-provided 'seqan::Shape > >::Shape(const seqan::Shape > >&) [with TValue = seqan::SimpleType]' + 281 | Shape(Shape const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >& seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::operator=(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 110 | target = source; + | ~~~~~~~^~~~~~~~ +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_base.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:69: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = char; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:241:45: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:46: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::AnchorGaps > >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecV = seqan::AnchorGaps > >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:471:31: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >, seqan::Tag >; TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Value::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::Reference > >::Type = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_paired_match_filter.h:160:64: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(const seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:357:37: required from 'typename seqan::Convert >, seqan::Proxy >::Type seqan::convertImpl(seqan::Convert >, T>, const seqan::Proxy&) [with THost = seqan::SimpleType; char CHAR = '-'; TSpec = seqan::Tag; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec2 = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >, seqan::Proxy >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: required from 'typename seqan::Convert::Type seqan::convert(const TSource&) [with TTarget = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >; TSource = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; typename seqan::Convert::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_alphabet_expansion.h:92:59: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:17: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: required from 'typename seqan::Convert >::Type seqan::convertImpl(seqan::Convert, const seqan::Proxy&) [with TTarget = char; T = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >; TSpec = seqan::IteratorProxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > >; typename seqan::Convert >::Type = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_conversion.h:149:23: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:45: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(const seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:314:32: required from 'typename seqan::Position > >::Type seqan::position(const seqan::ModifiedIterator >&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; typename seqan::Position > >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:675:73: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:288:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 288 | TContainer cont(container(host(me))); + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:275:20: required from 'typename seqan::GetValue > >::Type seqan::getValue(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >; typename seqan::GetValue > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_base.h:151:37: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorEditDistance]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1210:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TSpec = seqan::ModView > >; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:30: required from 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::SimpleType; TSeqVValue = seqan::SimpleType; TSeqVIterator = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:1076:24: required from 'void seqan::writeAlignments(seqan::FormattedFile, seqan::Tag, TSpec>&, seqan::FragmentStore&, TBamIOFunctor&) [with TSpec = void; TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TBamIOFunctor = seqan::BamAlignFunctorSemiGlobalGotoh]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1215:32: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazerSMode = seqan::RazerSMode; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1301:27: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSLocal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/outputFormat.h:1345:31: required from 'int seqan::dumpMatches(seqan::FragmentStore&, TCounts&, seqan::CharString, seqan::RazerSOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:257:20: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 278 | TContainer cont(container(host(me))); + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:62: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::UngappedShape<0> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:318:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::OneGappedShape>]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, const TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:889:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:924:24: required from 'void seqan::assign(seqan::Holder >&, const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:150:15: required from 'const seqan::Holder >& seqan::Holder >::operator=(const seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:519:11: required from 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSource = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; typename seqan::DisableIf > >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TValue2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3354:39: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3422:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:118:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 118 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:34, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:74: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >; TShapeSpec = seqan::Shape, seqan::GappedShape > >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 3%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesAll_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3431:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSGapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3443:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::UngappedShape<0> >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::UngappedShape<0> >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::UngappedShape<0> >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3376:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Pigeonhole >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >, seqan::Pigeonhole >, seqan::Shape, seqan::OneGappedShape>, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:85: +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TParam = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource1 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*; TSource2 = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3351:45: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TShape&, const TRazerSMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TShape = seqan::Shape, seqan::GappedShape > >; TRazerSMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3381:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, const TRazersMode&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TRazersMode = seqan::RazerSMode]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3396:25: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&, seqan::RazerSMode, TMatchNPolicy>) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>; TAlignMode = seqan::RazerSGlobal; TGapMode = seqan::RazerSUngapped; TMatchNPolicy = seqan::NMatchesNone_]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.h:3452:33: required from 'int seqan::_mapReads(seqan::FragmentStore&, TCounts&, seqan::RazerSCoreOptions&) [with TFSSpec = MyFragStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TCounts = seqan::String >; TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:235:26: required from 'int mapReads(seqan::StringSet > >&, seqan::StringSet > >&, seqan::RazerSOptions&) [with TSpec = seqan::RazerSSpec<>]' +/build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:866:66: required from here +/build/seqan2-2.4.0+dfsg/apps/razers3/razers_matepairs_parallel.h:84:7: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 84 | class ThreadLocalStorage > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:61: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/razers3/razers.cpp:60: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >::ThreadLocalStorage(seqan::ThreadLocalStorage, seqan::Alloc<> >, seqan::FragmentStore, seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >, seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >, seqan::Pattern, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >, seqan::IndexQGram, seqan::GappedShape > >, seqan::Tag > >, seqan::Swift > > >, seqan::Shape, seqan::GappedShape > >, seqan::RazerSCoreOptions >, seqan::String >, seqan::RazerSMode > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:46:14: required from 'bool _loadSequences(TSeqSet&, TNameSet&, const char*) [with TSeqSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >; TNameSet = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:66:19: required from 'void customizedMsaAlignment(const seqan::MsaOptions&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:290:31: required from 'void _initMsaParams(seqan::ArgumentParser&, TScore&) [with TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:305:40: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee/seqan_tcoffee.cpp:23: + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:524:97: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:544:95: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet > >, seqan::Owner > >; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer > >, seqan::Owner > >, void>, Db > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:456:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, Online) [with TText = seqan::StringSet > >, seqan::Owner > >; TSpec = seqan::Tag; TIndex = seqan::Index > >, seqan::Owner > >, seqan::IndexSa > >; Online = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:552:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TSpec = seqan::IndexSa >; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:195:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndexSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/finder.h:605:23: required from 'void execute(DbFinder >&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TDbQuerySpec = seqan::Tag; TDelegate = Writer, seqan::Alloc > >, seqan::Owner > >, void>, Db, seqan::Alloc > >, seqan::Owner > >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:330:12: required from 'int runSearcher(Options&, const TText&, const TIndex&, TSpec, const Nothing&) [with TText = seqan::StringSet, seqan::Alloc > >, seqan::Owner > >; TIndex = seqan::Index, seqan::Alloc > >, seqan::Owner > >, seqan::IndexSa > >; TSpec = seqan::Tag; seqan::Nothing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:516:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/db.h:43, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:61: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/apps/searchjoin/search.cpp:56: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -[ 3%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_app.cpp -[ 3%] Linking CXX executable ../../bin/sak -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target sak -make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/depend.internal". -Scanning dependencies of target snp_store -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 3%] Linking CXX executable ../../bin/param_chooser +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser && /usr/bin/cmake -E cmake_link_script CMakeFiles/param_chooser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/param_chooser.dir/param_chooser.cpp.o -o ../../bin/param_chooser -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -21436,6 +20790,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target param_chooser +make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/depend.internal". +Scanning dependencies of target sgip +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/sgip/CMakeFiles/sgip.dir/sgip.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/sgip.dir/sgip.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/sgip/sgip.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target pair_align_global_1000 +make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/depend.internal". +Scanning dependencies of target snp_store +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object apps/snp_store/CMakeFiles/snp_store.dir/snp_store.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/snp_store.dir/snp_store.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, @@ -21752,17 +21132,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, @@ -22167,6 +21536,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_genome.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, @@ -22568,9 +21939,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 3%] Linking CXX executable ../../bin/sam2matrix -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:44, @@ -22819,19 +22187,263 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 3%] Linking CXX executable ../../bin/razers3_simulate_reads +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_simulate_reads.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_simulate_reads.dir/simulate_reads.cpp.o -o ../../bin/razers3_simulate_reads -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target sam2matrix +[ 3%] Built target razers3_simulate_reads make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 3%] Linking CXX executable ../../bin/rabema_prepare_sam +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_prepare_sam.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_prepare_sam.dir/prepare_sam.cpp.o -o ../../bin/rabema_prepare_sam -lrt -lz -lbz2 Scanning dependencies of target stellar make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 3%] Building CXX object apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/stellar.dir/stellar.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp +[ 3%] Linking CXX executable ../../bin/razers3_quality2prob +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3_quality2prob.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3_quality2prob.dir/quality2prob.cpp.o -o ../../bin/razers3_quality2prob -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target rabema_prepare_sam +make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/depend.internal". +Scanning dependencies of target tree_recon +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build +[ 3%] Built target razers3_quality2prob +make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend.internal". +[ 3%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/tree_recon/tree_recon.cpp +Scanning dependencies of target test_align_simd_local_equal_length +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:106:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_genome.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Linking CXX executable ../../bin/rep_sep +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep && /usr/bin/cmake -E cmake_link_script CMakeFiles/rep_sep.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rep_sep.dir/rep_sep.cpp.o -o ../../bin/rep_sep -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target rep_sep +make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend.internal". +Scanning dependencies of target test_align_simd_global_variable_length +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp +[ 3%] Linking CXX executable ../../bin/sam2matrix +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix && /usr/bin/cmake -E cmake_link_script CMakeFiles/sam2matrix.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sam2matrix.dir/sam2matrix.cpp.o -o ../../bin/sam2matrix -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target sam2matrix +make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend.internal". +Scanning dependencies of target test_align_simd_local_variable_length +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:54, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -22872,6 +22484,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Linking CXX executable ../../bin/rabema_build_gold_standard +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_build_gold_standard.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_build_gold_standard.dir/rabema_build_gold_standard.cpp.o -o ../../bin/rabema_build_gold_standard -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -22897,15 +22512,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 3%] Linking CXX executable ../../bin/samcat +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target rabema_build_gold_standard +make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend.internal". +Scanning dependencies of target test_align_simd_global_equal_length +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp +[ 3%] Built target samcat +make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/depend.internal". +Scanning dependencies of target test_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align/CMakeFiles/test_align.dir/test_align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align.dir/test_align.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:31: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -22949,6 +22584,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 3%] Linking CXX executable ../../bin/sak +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak && /usr/bin/cmake -E cmake_link_script CMakeFiles/sak.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sak.dir/sak.cpp.o -o ../../bin/sak -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:33: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': @@ -22997,6 +22635,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target sak +make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/apps/snp_store/snp_store.cpp:33: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': @@ -23019,6 +22664,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = const seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +Scanning dependencies of target test_align_extend +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align_extend/CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -23100,6 +22751,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:80:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:68:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: @@ -23847,8 +23548,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -[ 3%] Linking CXX executable ../../bin/samcat -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat && /usr/bin/cmake -E cmake_link_script CMakeFiles/samcat.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:28: /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h: In instantiation of 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]': /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' @@ -24029,7 +23728,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/samcat.dir/samcat.cpp.o -o ../../bin/samcat -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:28: /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h: In instantiation of 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]': /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' @@ -24238,13 +23936,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target samcat -make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -24297,9 +23988,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target tree_recon -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -24323,7 +24011,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:28: /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h: In instantiation of 'void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]': /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:614:23: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' @@ -24343,8 +24030,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -[ 3%] Building CXX object apps/tree_recon/CMakeFiles/tree_recon.dir/tree_recon.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.4.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/tree_recon.dir/tree_recon.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/tree_recon/tree_recon.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -24784,6 +24469,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 3%] Linking CXX executable ../../bin/rabema_evaluate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema && /usr/bin/cmake -E cmake_link_script CMakeFiles/rabema_evaluate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/rabema_evaluate.dir/rabema_evaluate.cpp.o -o ../../bin/rabema_evaluate -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, @@ -24834,9 +24522,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 4%] Linking CXX executable ../../bin/sgip -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../bin/sgip -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:80:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:68:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, @@ -24887,6 +24622,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Built target rabema_evaluate +make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, @@ -24912,6 +24654,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target test_align_parallel_interface +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: @@ -24942,6 +24687,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 3%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_parallel/test_align_parallel_interface.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, @@ -25146,7 +24894,47 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:42, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:42, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, @@ -25198,12 +24986,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -[ 4%] Built target sgip -make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, @@ -25255,12 +25037,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -Scanning dependencies of target test_align_simd_local_equal_length -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 4%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: @@ -25360,6 +25136,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]' 143 | Index(Index const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h: In instantiation of 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:558:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 558 | TAlign align(alignOrig); + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:586:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 586 | TAlign align(alignOrig); + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:620:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 620 | TAlign align(alignOrig); + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25429,6 +25240,426 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]' 143 | Index(Index const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:504:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:178:36: required from 'void SEQAN_TEST_test_align_extend_simple_infixes_recomp() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:504:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:178:36: required from 'void SEQAN_TEST_test_align_extend_simple_infixes_recomp() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:569:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:415:24: required from 'void SEQAN_TEST_test_align_extend_xdrop() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:47:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:569:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:415:24: required from 'void SEQAN_TEST_test_align_extend_xdrop() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:47:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:603:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:514:24: required from 'void SEQAN_TEST_test_align_extend_xdrop_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:48:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:603:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:514:24: required from 'void SEQAN_TEST_test_align_extend_xdrop_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:48:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 294 | ModifiedString const r_inf0(inf0); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 295 | ModifiedString const r_inf1(inf1); + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25483,6 +25714,114 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h: In instantiation of 'seqan::Iter > seqan::operator++(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]': +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:183:11: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1157:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:156:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:205:39: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 205 | Iter > ret = it; + | ^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:207:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 207 | return ret; + | ^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h: In instantiation of 'seqan::Iter > seqan::operator--(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]': +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:219:11: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1157:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:156:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:226:39: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 226 | Iter > ret = it; + | ^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:228:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 228 | return ret; + | ^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]': +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:345:5: required from 'void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1171:43: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:158:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator-(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]': +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:346:5: required from 'void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1171:43: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:158:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:760:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 760 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:762:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 762 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25539,6 +25878,29 @@ | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_array.h:427:10: required from 'void seqan::assignSource(seqan::Gaps >&, const TSequence2&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TSequence2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:59:21: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +[ 3%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >]': @@ -25591,6 +25953,54 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25645,6 +26055,70 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:515:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:515:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:627:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:627:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25699,6 +26173,198 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of 'TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:72:28: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:167:36: required from 'void SEQAN_TEST_test_align_global_alignment_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:595:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 468 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 487 | finger2 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 489 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 518 | finger1 = begin(matrix_); + | ~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 543 | it_ = finger1; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:95:28: required from 'int seqan::globalAlignment(seqan::Align&, const MyersHirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:205:36: required from 'void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:599:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 348 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 368 | finger2 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 370 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 398 | finger1 = begin(matrix_); + | ~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 423 | it_ = finger1; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:104:28: required from 'int seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:231:36: required from 'void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:600:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 348 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 368 | finger2 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 370 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 398 | finger1 = begin(matrix_); + | ~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 423 | it_ = finger1; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25753,6 +26419,126 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:167:28: required from 'int seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersHirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; seqan::MyersHirschberg = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:311:31: required from 'void SEQAN_TEST_test_align_global_alignment_score_myers_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:606:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 348 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 368 | finger2 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 370 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 398 | finger1 = begin(matrix_); + | ~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 423 | it_ = finger1; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25899,6 +26685,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:226:43: required from 'typename seqan::Reference > >::Type seqan::Gaps >::operator[](seqan::Gaps >::TPosition_) [with TSource = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; typename seqan::Reference > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >; seqan::Gaps >::TPosition_ = int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:205:9: required from 'void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:1633:40: required from 'void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:104:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::GapsIterator >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:835:5: required from 'void testAlignGapsIteratorInterfaceBegin(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:1682:40: required from 'void SEQAN_TEST_test_align_gaps_anchor_gaps_iterator_interface_begin() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:111:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, @@ -25926,6 +26746,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h: In instantiation of 'void seqan::goEnd(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:10: required from 'void seqan::goEnd(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:274:14: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1062:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:142:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:415:8: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 415 | it = end(container); + | ~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]' + 91 | Iter(Iter const & other) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h: In instantiation of 'void seqan::goBegin(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:403:12: required from 'void seqan::goBegin(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:281:16: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1062:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:142:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:387:8: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 387 | it = begin(container); + | ~~~^~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]' + 91 | Iter(Iter const & other) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -26225,2112 +27079,145 @@ from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:604:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:604:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' -/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:80:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:68:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_equal_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -[ 5%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp -[ 5%] Linking CXX executable ../../bin/razers -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 5%] Built target razers -make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend.internal". -Scanning dependencies of target test_align_simd_global_variable_length -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 5%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:80:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:68:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -[ 6%] Linking CXX executable ../../bin/tree_recon -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Built target tree_recon -make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend.internal". -Scanning dependencies of target test_align_simd_local_variable_length -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Building CXX object tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:80:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::LocalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig<>; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local.h:68:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_local_variable_length.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -[ 6%] Linking CXX executable ../../bin/test_align_simd_local_equal_length -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_equal_length.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -o ../../bin/test_align_simd_local_equal_length -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Built target test_align_simd_local_equal_length -make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend.internal". -Scanning dependencies of target test_align_simd_global_equal_length -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Building CXX object tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:80:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:68:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -[ 6%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_options.cpp -[ 6%] Linking CXX executable ../../bin/snp_store -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../bin/snp_store -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Built target snp_store -make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/depend.internal". -Scanning dependencies of target test_align -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 6%] Building CXX object tests/align/CMakeFiles/test_align.dir/test_align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align.dir/test_align.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp -[ 7%] Linking CXX executable ../../bin/test_align_simd_local_variable_length -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_variable_length.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -o ../../bin/test_align_simd_local_variable_length -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Built target test_align_simd_local_variable_length -make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/depend.internal". -Scanning dependencies of target test_align_extend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Building CXX object tests/align_extend/CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h: In instantiation of 'seqan::Iter > seqan::operator++(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]': -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:183:11: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1157:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:156:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:205:39: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 205 | Iter > ret = it; - | ^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:207:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 207 | return ret; - | ^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h: In instantiation of 'seqan::Iter > seqan::operator--(seqan::Iter >&, int) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::AnchorGaps<>]': -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:219:11: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1157:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:156:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:226:39: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 226 | Iter > ret = it; - | ^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:83, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_base.h:228:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 228 | return ret; - | ^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]': -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:345:5: required from 'void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1171:43: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:158:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator-(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; TDifference = int]': -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:346:5: required from 'void testAlignGapsIteratorPointerArithmetic(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1171:43: required from 'void SEQAN_TEST_test_align_gaps_iterator_anchor_pointer_arithmetic() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:158:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:760:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 760 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:762:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 762 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:515:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:515:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:627:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::Blosum62_>; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_local.h:627:9: required from 'void SEQAN_TEST_test_align_local_alignment_enumeration_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:501:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of 'TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:72:28: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score >&, const Hirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; seqan::Hirschberg = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:167:36: required from 'void SEQAN_TEST_test_align_global_alignment_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:595:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:468:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 468 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:487:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 487 | finger2 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:489:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 489 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:518:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 518 | finger1 = begin(matrix_); - | ~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h:543:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 543 | it_ = finger1; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:95:28: required from 'int seqan::globalAlignment(seqan::Align&, const MyersHirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:205:36: required from 'void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_align() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:599:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 348 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 368 | finger2 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 370 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 398 | finger1 = begin(matrix_); - | ~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 423 | it_ = finger1; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:104:28: required from 'int seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:231:36: required from 'void SEQAN_TEST_test_align_global_alignment_myers_hirschberg_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:600:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 348 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 368 | finger2 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 370 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 398 | finger1 = begin(matrix_); - | ~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 423 | it_ = finger1; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = const seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = const seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:167:28: required from 'int seqan::globalAlignmentScore(const seqan::String&, const seqan::String&, const MyersHirschberg&) [with TAlphabetH = seqan::SimpleType; TSpecH = seqan::Alloc<>; TAlphabetV = seqan::SimpleType; TSpecV = seqan::Alloc<>; seqan::MyersHirschberg = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_global_alignment_specialized.h:311:31: required from 'void SEQAN_TEST_test_align_global_alignment_score_myers_hirschberg() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:606:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 348 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 368 | finger2 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 370 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 398 | finger1 = begin(matrix_); - | ~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 423 | it_ = finger1; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:226:43: required from 'typename seqan::Reference > >::Type seqan::Gaps >::operator[](seqan::Gaps >::TPosition_) [with TSource = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; typename seqan::Reference > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >; seqan::Gaps >::TPosition_ = int]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:205:9: required from 'void testAlignGapsGapOperationsGapCenter(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:1633:40: required from 'void SEQAN_TEST_test_align_gaps_anchor_gaps_gap_operations_gaps_center() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:104:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TSpec = seqan::GapsIterator >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:835:5: required from 'void testAlignGapsIteratorInterfaceBegin(const TGapsSpec&) [with TGapsSpec = seqan::AnchorGaps<>]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps.h:1682:40: required from 'void SEQAN_TEST_test_align_gaps_anchor_gaps_iterator_interface_begin() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:111:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps<> >, seqan::GapsIterator > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h: In instantiation of 'void seqan::goEnd(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:430:10: required from 'void seqan::goEnd(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:274:14: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1062:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:142:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:415:8: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 415 | it = end(container); - | ~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]' - 91 | Iter(Iter const & other) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h: In instantiation of 'void seqan::goBegin(TIterator&, TContainer&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >; TContainer = seqan::Gaps, seqan::Alloc<> > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:403:12: required from 'void seqan::goBegin(TIterator&) [with TIterator = seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:281:16: required from 'void testAlignGapsIteratorMovement(const TGapsSpec&) [with TGapsSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align_gaps_iterator.h:1062:34: required from 'void SEQAN_TEST_test_align_gaps_iterator_array_movement() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:142:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_interface.h:387:8: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 387 | it = begin(container); - | ~~~^~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, - from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> > >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> > >]' - 91 | Iter(Iter const & other) : - | ^~~~ + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:604:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:60: /build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of 'bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = false; bool FreeLeft = false; bool FreeRight = false; bool FreeBottom = false; TACSpec = seqan::Tag; TScore = int]': /build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from 'void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig<>]' @@ -28376,6 +27263,34 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' 91 | Iter(Iter const & other) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String, seqan::Alloc<> >; TSeed = seqan::Seed >; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:60: /build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_dynamic_gap.h: In instantiation of 'bool _validateAlignment(const TAlignment&, const seqan::AlignConfig&, const TScore&, const seqan::Score >&) [with TAlignment = seqan::Align, seqan::Alloc<> > >; bool FreeTop = false; bool FreeLeft = true; bool FreeRight = true; bool FreeBottom = false; TACSpec = seqan::Tag; TScore = int]': /build/seqan2-2.4.0+dfsg/tests/align/test_alignment_algorithms_dynamic_gap.h:194:9: required from 'void testDynamicGapInterfaces(TAlign&, const TAlgorithm&, const TAlignConfig&, int, int) [with TAlign = seqan::Align, seqan::Alloc<> > >; TAlgorithm = seqan::Tag; TAlignConfig = seqan::AlignConfig]' @@ -28586,6 +27501,97 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -28690,6 +27696,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:604:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -28719,6 +27752,151 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: required from 'void _fillMatrixBestEndsLeft(TMatrix&, seqan::String&, const seqan::Segment&, const seqan::Segment&, TSeed&, TSeed&, const TScore&) [with TMatrix = seqan::String >; TPossEnd = ExtensionEndPosition; TSequence = seqan::String >; TSeed = seqan::Seed >; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:697:26: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::AlignExtend_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn<>; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:157:33: required from 'TScoreValue seqan::_setUpAndRunAlignImpl(TAliExtContext_&, const TString0&, const TString1&, const seqan::Score&, int, int, TScoreValue, const TTracebackConfig&, const seqan::True&, const seqan::False&) [with TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:351:43: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -28736,47 +27914,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:42, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:42, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -29119,6 +28256,78 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: @@ -29173,6 +28382,396 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps<> >, seqan::GapsIterator > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps<> >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSeqHValue = char; TSeqVValue = char; TSeqVIterator = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_, seqan::Tag, seqan::TracebackOn<>, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::AlignExtend_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn<>; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:157:33: required from 'TScoreValue seqan::_setUpAndRunAlignImpl(TAliExtContext_&, const TString0&, const TString1&, const seqan::Score&, int, int, TScoreValue, const TTracebackConfig&, const seqan::True&, const seqan::False&) [with TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >; TString0 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TString1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 278 | TContainer cont(container(host(me))); + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:650:29: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:99:44: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -29386,41 +28985,151 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h: In instantiation of 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:558:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 558 | TAlign align(alignOrig); - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:586:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 586 | TAlign align(alignOrig); - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:620:16: warning: implicitly-declared 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >::Align(const seqan::Align >, seqan::InfixSegment>, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 620 | TAlign align(alignOrig); - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:41, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:503:103: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:685:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -29439,6 +29148,91 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:687:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, from /build/seqan2-2.4.0+dfsg/tests/align/test_align_stream.h:40, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:38: @@ -29505,571 +29299,396 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:504:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:178:36: required from 'void SEQAN_TEST_test_align_extend_simple_infixes_recomp() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:504:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:178:36: required from 'void SEQAN_TEST_test_align_extend_simple_infixes_recomp() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:569:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:415:24: required from 'void SEQAN_TEST_test_align_extend_xdrop() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:47:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:689:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:569:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:415:24: required from 'void SEQAN_TEST_test_align_extend_xdrop() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:47:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:603:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:514:24: required from 'void SEQAN_TEST_test_align_extend_xdrop_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:48:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:691:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:434:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:603:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:514:24: required from 'void SEQAN_TEST_test_align_extend_xdrop_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:48:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 294 | ModifiedString const r_inf0(inf0); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:43, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:295:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 295 | ModifiedString const r_inf1(inf1); - | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:294:49: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TPattern = seqan::Pattern, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = seqan::SimpleType]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:693:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_array.h:427:10: required from 'void seqan::assignSource(seqan::Gaps >&, const TSequence2&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TSequence2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:59:21: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:44, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment >, seqan::InfixSegment>; TString2 = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar_extension.h:396:13: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:56:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:190:33: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&, const TAlgoTag&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_unbanded.h:218:31: required from 'TScoreValue seqan::globalAlignment(seqan::Align&, const seqan::Score&, const seqan::AlignConfig&) [with TSequence = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:554:20: required from 'void SEQAN_TEST_test_align_extend_semiglobal() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_<>; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:458:17: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, BandedGlobal) [with TInfix = seqan::Segment >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TSource = seqan::String >; TId = seqan::String >; BandedGlobal = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:64:16: required from 'bool _stellarOnOne(TSequence&, TId&, TPattern&, bool, TMatches&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >; TPattern = seqan::Pattern >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >, seqan::Swift > >; TMatches = seqan::StringSet >, seqan::String > > >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:174:31: required from 'bool _stellarOnAll(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, StellarOptions&) [with TSequence = seqan::String >; TId = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:655:23: required from 'int mainWithOptions(TOptions&, seqan::String) [with TOptions = StellarOptions; TAlphabet = char]' +/build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:695:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/stellar/stellar.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::InfixSegment>]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:80:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:68:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_variable_length.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:35: @@ -30136,32 +29755,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::AlignExtend_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn<>; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:157:33: required from 'TScoreValue seqan::_setUpAndRunAlignImpl(TAliExtContext_&, const TString0&, const TString1&, const seqan::Score&, int, int, TScoreValue, const TTracebackConfig&, const seqan::True&, const seqan::False&) [with TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >; TString0 = seqan::Segment >, seqan::InfixSegment>; TString1 = seqan::Segment >, seqan::InfixSegment>; TScoreValue = int; TScoreSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:351:43: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -30396,39 +29989,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 7%] Linking CXX executable ../../bin/seqcons2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h: In instantiation of 'typename seqan::Container >::Type seqan::container(seqan::ModifiedIterator&) [with THost = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; TSpec = seqan::Tag; typename seqan::Container >::Type = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:397:81: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSeqHValue = char; TSeqVValue = char; TSeqVIterator = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >; TScoringScheme = seqan::Score >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_, seqan::Tag, seqan::TracebackOn<>, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:891:38: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::AlignExtend_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn<>; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:157:33: required from 'TScoreValue seqan::_setUpAndRunAlignImpl(TAliExtContext_&, const TString0&, const TString1&, const seqan::Score&, int, int, TScoreValue, const TTracebackConfig&, const seqan::True&, const seqan::False&) [with TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >; TString0 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TString1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:536:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:287:24: required from 'void SEQAN_TEST_test_align_extend_banded() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_iterator.h:278:16: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 278 | TContainer cont(container(host(me))); - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' @@ -30479,66 +30039,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:503:103: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TSequenceV = seqan::ModifiedString >, seqan::InfixSegment>, seqan::Tag >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:297:42: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:395:32: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:424:36: required from 'TScoreValue seqan::_extendAlignmentImpl(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::False; TBoolXDrop = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h:519:32: required from 'TScoreValue seqan::extendAlignment(seqan::Align&, const TScoreValue&, const TString&, const TString&, const seqan::Tuple&, const seqan::ExtensionDirection&, const seqan::Score&) [with TStringInfix = seqan::Segment >, seqan::InfixSegment>; TAlignSpec = seqan::Tag; TString = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.h:65:32: required from 'void SEQAN_TEST_test_align_extend_simple() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/align_extend/test_align_extend.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/align/test_align.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -30770,19 +30270,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Built target seqcons2 -make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend.internal". -Scanning dependencies of target test_align_parallel_interface -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_parallel/test_align_parallel_interface.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::ScoreMatrix, seqan::ScoreSpecSelectable>; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:91:36: required from 'void SimdAlignTestCommon__Dynamic_Score_Matrix_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:80:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TParam = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource1 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*; TSource2 = seqan::Align, seqan::Alloc<> >, seqan::Tag >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_base.h:1301:18: required from 'typename seqan::Size >::Type seqan::resize(seqan::StringSet&, TSize, seqan::Tag) [with TString = seqan::Align, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::Owner<>; TSize = unsigned int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::StringSet, seqan::Alloc<> >, seqan::Tag >, seqan::Owner<> >&; TSize = unsigned int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:166:11: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, int, int) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:216:33: required from 'void testAlignSimd(const TFunctor&, const seqan::Score&, const TAlignConfig&, const TSimdLength&, const TBandFlag&) [with TAlphabet = seqan::SimpleType; TFunctor = impl::test_align_simd::GlobalAlignTester_; TScoreValue = int; TScoreSpec = seqan::Tag; TAlignConfig = seqan::AlignConfig; TSimdLength = seqan::Tag; TBandFlag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:74:30: required from 'void SimdAlignTestCommon__Affine_Align::runTest() [with SEQAN_TParam = std::tuple >, seqan::Tag, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global.h:68:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_base.h:41, + from /build/seqan2-2.4.0+dfsg/tests/align/test_align_simd_global_equal_length.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -30807,43 +30344,242 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -[ 7%] Linking CXX executable ../../bin/s4_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lrt -lz -lbz2 -[ 7%] Linking CXX executable ../../bin/s4_join -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 4%] Linking CXX executable ../../bin/sgip +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip && /usr/bin/cmake -E cmake_link_script CMakeFiles/sgip.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/sgip.dir/sgip.cpp.o -o ../../bin/sgip -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Built target s4_search +[ 4%] Built target sgip make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/DependInfo.cmake --color= -[ 7%] Built target s4_join +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend.internal". +Scanning dependencies of target test_align_parallel_algorithm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 4%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_parallel/test_align_parallel_algorithm.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 141 | _cargo() + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:64: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:56: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:193:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:264:64: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_illumina.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 4%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp +[ 4%] Linking CXX executable ../../bin/test_align_parallel_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_algorithm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o -o ../../bin/test_align_parallel_algorithm -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 4%] Built target test_align_parallel_algorithm make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/depend.internal". Scanning dependencies of target test_align_parallel_data_structures -Scanning dependencies of target test_align_parallel_algorithm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_parallel/test_align_parallel_algorithm.cpp -[ 7%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/test_align_parallel_data_structures.cpp.o +[ 4%] Building CXX object tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/test_align_parallel_data_structures.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_parallel_data_structures.dir/test_align_parallel_data_structures.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_parallel/test_align_parallel_data_structures.cpp -[ 8%] Linking CXX executable ../../bin/test_align_parallel_data_structures -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_data_structures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_data_structures.dir/test_align_parallel_data_structures.cpp.o -o ../../bin/test_align_parallel_data_structures -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 5%] Linking CXX executable ../../bin/tree_recon +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree_recon.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/tree_recon.dir/tree_recon.cpp.o -o ../../bin/tree_recon -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_parallel_data_structures +[ 5%] Built target tree_recon make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_profile /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile/CMakeFiles/test_align_profile.dir/DependInfo.cmake --color= @@ -30853,24 +30589,183 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/align_profile/CMakeFiles/test_align_profile.dir/test_align_profile.cpp.o +[ 5%] Building CXX object tests/align_profile/CMakeFiles/test_align_profile.dir/test_align_profile.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_profile.dir/test_align_profile.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_profile/test_align_profile.cpp -[ 8%] Linking CXX executable ../../bin/test_align_parallel_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_algorithm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_algorithm.dir/test_align_parallel_algorithm.cpp.o -o ../../bin/test_align_parallel_algorithm -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_parallel_algorithm -make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/depend.internal". -Scanning dependencies of target test_align_split -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/align_split/CMakeFiles/test_align_split.dir/test_align_split.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_split.dir/test_align_split.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 141 | _cargo() + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:64: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: required from 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:56: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::ModView > >; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >; TTagSpec = seqan::Standard_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >, seqan::ModView > > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:59:25: required from 'void {anonymous}::_simulateSequence(TRead&, TRng&, const TFrag&, const TCigarString&) [with TFrag = seqan::ModifiedString, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >; TRead = seqan::String, seqan::Alloc<> >; TRng = std::mersenne_twister_engine; TCigarString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:153:64: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/simulate_sanger.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/align_profile/test_align_profile.cpp:35: @@ -30912,6 +30807,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 5%] Building CXX object apps/mason2/CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp +[ 6%] Linking CXX executable ../../bin/test_align_parallel_data_structures +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_data_structures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_data_structures.dir/test_align_parallel_data_structures.cpp.o -o ../../bin/test_align_parallel_data_structures -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 6%] Built target test_align_parallel_data_structures +make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/depend.internal". +Scanning dependencies of target test_align_split +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 6%] Building CXX object tests/align_split/CMakeFiles/test_align_split.dir/test_align_split.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_align_split.dir/test_align_split.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/align_split/test_align_split.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:55, from /build/seqan2-2.4.0+dfsg/tests/align_profile/test_align_profile.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/align_profile/add_to_profile.h: In instantiation of 'void seqan::addToProfile(seqan::String >&, seqan::String&, int, int) [with TChar = seqan::SimpleType; TValue = int; TSpec = void; TSpec2 = seqan::Alloc<>]': @@ -30998,14 +30911,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 8%] Linking CXX executable ../../bin/test_align_profile -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_profile.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_profile.dir/test_align_profile.cpp.o -o ../../bin/test_align_profile -lrt -lz -lbz2 -[ 8%] Linking CXX executable ../../bin/test_align_extend -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_extend.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o -o ../../bin/test_align_extend -lrt -lz -lbz2 +[ 6%] Linking CXX executable ../../bin/test_align_simd_local_equal_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_equal_length.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_equal_length.dir/test_align_simd_local_equal_length.cpp.o -o ../../bin/test_align_simd_local_equal_length -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_profile +[ 6%] Built target test_align_simd_local_equal_length make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free/CMakeFiles/test_alignment_free.dir/DependInfo.cmake --color= @@ -31015,10 +30925,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/alignment_free/CMakeFiles/test_alignment_free.dir/test_alignment_free.cpp.o +[ 6%] Building CXX object tests/alignment_free/CMakeFiles/test_alignment_free.dir/test_alignment_free.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_alignment_free.dir/test_alignment_free.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/alignment_free/test_alignment_free.cpp +[ 6%] Linking CXX executable ../../bin/test_align_extend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_extend.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_extend.dir/test_align_extend.cpp.o -o ../../bin/test_align_extend -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_extend +[ 6%] Built target test_align_extend make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/DependInfo.cmake --color= @@ -31028,11 +30941,36 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/test_arg_parse_version_check.cpp.o +[ 6%] Building CXX object tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/test_arg_parse_version_check.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_arg_parse_version_check.dir/test_arg_parse_version_check.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse_version_check.cpp -[ 8%] Linking CXX executable ../../bin/seqan_tcoffee -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 6%] Linking CXX executable ../../bin/test_align_parallel_interface +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_interface.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o -o ../../bin/test_align_parallel_interface -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 6%] Built target test_align_parallel_interface +make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend.internal". +Scanning dependencies of target test_arg_parse +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 6%] Building CXX object tests/arg_parse/CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/alignment_free/test_alignment_free.cpp:37: @@ -31072,6 +31010,121 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 7%] Linking CXX executable ../../bin/test_align_simd_local_variable_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_local_variable_length.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_local_variable_length.dir/test_align_simd_local_variable_length.cpp.o -o ../../bin/test_align_simd_local_variable_length -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 7%] Built target test_align_simd_local_variable_length +make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target test_bam_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 7%] Building CXX object tests/bam_io/CMakeFiles/test_bam_io.dir/test_bam_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_bam_io.dir/test_bam_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:41, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:167:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:40, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free.h:59, from /build/seqan2-2.4.0+dfsg/tests/alignment_free/test_alignment_free.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h: In instantiation of 'void seqan::_alignmentFreeComparison(seqan::Matrix&, const TStringSet&, const seqan::AFScore >&) [with TValue = double; TStringSet = seqan::StringSet, seqan::Alloc<> > >]': @@ -31087,40 +31140,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >]' 105 | Iter(Iter const & other_) : | ^~~~ -[ 8%] Linking CXX executable ../../bin/test_align_parallel_interface -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_parallel_interface.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target seqan_tcoffee -make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_parallel_interface.dir/test_align_parallel_interface.cpp.o -o ../../bin/test_align_parallel_interface -lrt -lz -lbz2 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend.internal". -Scanning dependencies of target test_arg_parse -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/arg_parse/CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/arg_parse/test_arg_parse.cpp -[ 8%] Linking CXX executable ../../bin/stellar -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../bin/stellar -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_parallel_interface -make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/depend.internal". -Scanning dependencies of target test_bam_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/bam_io/CMakeFiles/test_bam_io.dir/test_bam_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_bam_io.dir/test_bam_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp +[ 7%] Linking CXX executable ../../bin/test_align_profile +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_profile.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_profile.dir/test_align_profile.cpp.o -o ../../bin/test_align_profile -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target stellar +[ 7%] Built target test_align_profile make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_exception.dir/DependInfo.cmake --color= @@ -31130,11 +31154,10 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/basic/CMakeFiles/test_basic_exception.dir/test_basic_exception.cpp.o +[ 7%] Building CXX object tests/basic/CMakeFiles/test_basic_exception.dir/test_basic_exception.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_exception.dir/test_basic_exception.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_exception.cpp -[ 8%] Linking CXX executable ../../bin/test_basic_exception -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_exception.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_exception.dir/test_basic_exception.cpp.o -o ../../bin/test_basic_exception -lrt -lz -lbz2 +[ 8%] Building CXX object apps/razers/CMakeFiles/razers.dir/param_tabs.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers.dir/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -31157,19 +31180,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_basic_exception -make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend.internal". -Scanning dependencies of target test_basic_metaprogramming -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Building CXX object tests/basic/CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_metaprogramming.cpp +[ 8%] Linking CXX executable ../../bin/test_basic_exception +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_exception.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_exception.dir/test_basic_exception.cpp.o -o ../../bin/test_basic_exception -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -31193,6 +31206,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 8%] Built target test_basic_exception +make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend.internal". +Scanning dependencies of target test_basic_metaprogramming +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 8%] Building CXX object tests/basic/CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_metaprogramming.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -31210,8 +31236,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 8%] Linking CXX executable ../../bin/test_align_split -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_split.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp:35: @@ -31230,7 +31254,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_split.dir/test_align_split.cpp.o -o ../../bin/test_align_split -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/bam_io/test_bam_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': @@ -31277,8 +31300,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 8%] Linking CXX executable ../../bin/test_basic_metaprogramming +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_metaprogramming.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o -o ../../bin/test_basic_metaprogramming -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_align_split +[ 8%] Built target test_basic_metaprogramming make -f tests/basic/CMakeFiles/test_basic_concept.dir/build.make tests/basic/CMakeFiles/test_basic_concept.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_concept.dir/DependInfo.cmake --color= @@ -31290,11 +31316,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 8%] Building CXX object tests/basic/CMakeFiles/test_basic_concept.dir/test_basic_concept.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_concept.dir/test_basic_concept.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_concept.cpp -[ 8%] Linking CXX executable ../../bin/test_basic_metaprogramming -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_metaprogramming.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_metaprogramming.dir/test_basic_metaprogramming.cpp.o -o ../../bin/test_basic_metaprogramming -lrt -lz -lbz2 +[ 8%] Linking CXX executable ../../bin/razers +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers.dir/razers.cpp.o CMakeFiles/razers.dir/param_tabs.cpp.o -o ../../bin/razers -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_basic_metaprogramming +[ 8%] Built target razers make -f tests/basic/CMakeFiles/test_basic_fundamental.dir/build.make tests/basic/CMakeFiles/test_basic_fundamental.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_fundamental.dir/DependInfo.cmake --color= @@ -31347,32 +31373,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 8%] Linking CXX executable ../../bin/test_alignment_free -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_free.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_alignment_free.dir/test_alignment_free.cpp.o -o ../../bin/test_alignment_free -lrt -lz -lbz2 [ 8%] Linking CXX executable ../../bin/test_basic_concept cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_concept.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_concept.dir/test_basic_concept.cpp.o -o ../../bin/test_basic_concept -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 8%] Built target test_basic_concept make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/DependInfo.cmake --color= -[ 8%] Built target test_alignment_free -make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/depend.internal". Scanning dependencies of target test_basic_alphabet make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 8%] Building CXX object tests/basic/CMakeFiles/test_basic_alphabet.dir/test_basic_alphabet.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_alphabet.dir/test_basic_alphabet.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_alphabet.cpp +[ 8%] Linking CXX executable ../../bin/test_alignment_free +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_free.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_alignment_free.dir/test_alignment_free.cpp.o -o ../../bin/test_alignment_free -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 8%] Built target test_alignment_free +make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/depend.internal". Scanning dependencies of target test_basic_aggregate make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/build @@ -31395,6 +31421,26 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 9%] Building CXX object tests/basic/CMakeFiles/test_basic_allocator.dir/test_basic_allocator.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_allocator.dir/test_basic_allocator.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_allocator.cpp +[ 9%] Building CXX object apps/seqcons2/CMakeFiles/seqcons2.dir/seqcons_options.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/seqcons2/seqcons_options.cpp +[ 9%] Linking CXX static library libmason_sim.a +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -P CMakeFiles/mason_sim.dir/cmake_clean_target.cmake +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_sim.dir/link.txt --verbose=1 +/usr/bin/ar qc libmason_sim.a CMakeFiles/mason_sim.dir/external_split_merge.cpp.o CMakeFiles/mason_sim.dir/genomic_variants.cpp.o CMakeFiles/mason_sim.dir/mason_options.cpp.o CMakeFiles/mason_sim.dir/methylation_levels.cpp.o CMakeFiles/mason_sim.dir/simulate_454.cpp.o CMakeFiles/mason_sim.dir/simulate_base.cpp.o CMakeFiles/mason_sim.dir/simulate_genome.cpp.o CMakeFiles/mason_sim.dir/simulate_illumina.cpp.o CMakeFiles/mason_sim.dir/simulate_sanger.cpp.o CMakeFiles/mason_sim.dir/vcf_materialization.cpp.o +/usr/bin/ranlib libmason_sim.a +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 9%] Built target mason_sim +make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/depend.internal". +Scanning dependencies of target test_basic_proxy +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 9%] Building CXX object tests/basic/CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_proxy.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:46, from /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_aggregate.cpp:38: @@ -31409,27 +31455,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = int; T2 = int; T3 = int]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 9%] Linking CXX executable ../../bin/test_basic_allocator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_allocator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_allocator.dir/test_basic_allocator.cpp.o -o ../../bin/test_basic_allocator -lrt -lz -lbz2 [ 9%] Linking CXX executable ../../bin/test_basic_alphabet cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_alphabet.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_alphabet.dir/test_basic_alphabet.cpp.o -o ../../bin/test_basic_alphabet -lrt -lz -lbz2 -[ 9%] Built target test_basic_allocator -make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/depend.internal". -Scanning dependencies of target test_basic_proxy -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 9%] Building CXX object tests/basic/CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_proxy.cpp +[ 10%] Linking CXX executable ../../bin/test_basic_proxy +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_proxy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o -o ../../bin/test_basic_proxy -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 9%] Built target test_basic_alphabet +[ 10%] Built target test_basic_alphabet make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_parallelism.dir/DependInfo.cmake --color= @@ -31439,45 +31472,42 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 9%] Building CXX object tests/basic/CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_parallelism.cpp -[ 10%] Linking CXX executable ../../bin/test_basic_aggregate -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_aggregate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_aggregate.dir/test_basic_aggregate.cpp.o -o ../../bin/test_basic_aggregate -lrt -lz -lbz2 -[ 10%] Linking CXX executable ../../bin/test_basic_parallelism -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_parallelism.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o -o ../../bin/test_basic_parallelism -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 10%] Built target test_basic_parallelism +[ 10%] Building CXX object tests/basic/CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_parallelism.cpp +[ 10%] Built target test_basic_proxy make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/DependInfo.cmake --color= -[ 10%] Built target test_basic_aggregate -make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/depend Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/depend.internal". -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake --color= Scanning dependencies of target test_basic_math make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/depend.internal". [ 10%] Building CXX object tests/basic/CMakeFiles/test_basic_math.dir/test_basic_math.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_math.dir/test_basic_math.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_math.cpp +[ 10%] Linking CXX executable ../../bin/test_basic_allocator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_allocator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_allocator.dir/test_basic_allocator.cpp.o -o ../../bin/test_basic_allocator -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 10%] Built target test_basic_allocator +make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/depend.internal". Scanning dependencies of target test_basic_iterator make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 10%] Building CXX object tests/basic/CMakeFiles/test_basic_iterator.dir/test_basic_iterator.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_iterator.dir/test_basic_iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_iterator.cpp -[ 11%] Linking CXX executable ../../bin/test_basic_proxy -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_proxy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_proxy.dir/test_basic_proxy.cpp.o -o ../../bin/test_basic_proxy -lrt -lz -lbz2 +[ 10%] Linking CXX executable ../../bin/test_basic_parallelism +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_parallelism.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_parallelism.dir/test_basic_parallelism.cpp.o -o ../../bin/test_basic_parallelism -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_proxy +[ 10%] Built target test_basic_parallelism make -f tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build.make tests/basic/CMakeFiles/test_basic_smart_pointer.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_smart_pointer.dir/DependInfo.cmake --color= @@ -31487,14 +31517,24 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build.make tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/basic/CMakeFiles/test_basic_smart_pointer.dir/test_basic_smart_pointer.cpp.o +[ 10%] Building CXX object tests/basic/CMakeFiles/test_basic_smart_pointer.dir/test_basic_smart_pointer.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_smart_pointer.dir/test_basic_smart_pointer.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_smart_pointer.cpp -[ 11%] Linking CXX executable ../../bin/test_arg_parse_version_check -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_arg_parse_version_check.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_arg_parse_version_check.dir/test_arg_parse_version_check.cpp.o -o ../../bin/test_arg_parse_version_check -lrt -lz -lbz2 -[ 11%] Linking CXX executable ../../bin/test_basic_math +[ 10%] Linking CXX executable ../../bin/test_basic_math cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_math.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_math.dir/test_basic_math.cpp.o -o ../../bin/test_basic_math -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 10%] Built target test_basic_math +make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/depend.internal". +Scanning dependencies of target test_basic_container +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 10%] Building CXX object tests/basic/CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_container.cpp In file included from /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_iterator.cpp:40: /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_iterator.h: In instantiation of 'void SEQAN_TEST_test_basic_iterator_position_arithmetics() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_iterator.cpp:71:5: required from here @@ -31532,22 +31572,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = int*]' 105 | Iter(Iter const & other_) : | ^~~~ +[ 10%] Linking CXX executable ../../bin/test_basic_container +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_container.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o -o ../../bin/test_basic_container -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_math -make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target test_basic_container -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_arg_parse_version_check +[ 10%] Built target test_basic_container make -f tests/bed_io/CMakeFiles/test_bed_io.dir/build.make tests/bed_io/CMakeFiles/test_bed_io.dir/depend -[ 11%] Building CXX object tests/basic/CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/basic/test_basic_container.cpp make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/bed_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io/CMakeFiles/test_bed_io.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io/CMakeFiles/test_bed_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io/CMakeFiles/test_bed_io.dir/depend.internal". @@ -31556,13 +31586,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/bed_io/CMakeFiles/test_bed_io.dir/build.make tests/bed_io/CMakeFiles/test_bed_io.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/bed_io/CMakeFiles/test_bed_io.dir/test_bed_io.cpp.o +[ 10%] Building CXX object tests/bed_io/CMakeFiles/test_bed_io.dir/test_bed_io.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_bed_io.dir/test_bed_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/bed_io/test_bed_io.cpp -[ 11%] Linking CXX executable ../../bin/test_basic_container -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_container.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_container.dir/test_basic_container.cpp.o -o ../../bin/test_basic_container -lrt -lz -lbz2 +[ 10%] Linking CXX executable ../../bin/test_align_split +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_split.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_split.dir/test_align_split.cpp.o -o ../../bin/test_align_split -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_container +[ 10%] Built target test_align_split make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/blast /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast/CMakeFiles/test_blast.dir/DependInfo.cmake --color= @@ -31572,8 +31602,56 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/blast/CMakeFiles/test_blast.dir/test_blast.cpp.o +[ 10%] Building CXX object tests/blast/CMakeFiles/test_blast.dir/test_blast.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_blast.dir/test_blast.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp +[ 11%] Linking CXX executable ../../bin/test_basic_aggregate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_aggregate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_aggregate.dir/test_basic_aggregate.cpp.o -o ../../bin/test_basic_aggregate -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Built target test_basic_aggregate +make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/depend.internal". +Scanning dependencies of target test_consensus +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Building CXX object tests/consensus/CMakeFiles/test_consensus.dir/test_consensus.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_consensus.dir/test_consensus.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp +[ 11%] Linking CXX executable ../../bin/test_basic_smart_pointer +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_smart_pointer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_smart_pointer.dir/test_basic_smart_pointer.cpp.o -o ../../bin/test_basic_smart_pointer -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Built target test_basic_smart_pointer +make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend.internal". +Scanning dependencies of target test_consensus_v2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Building CXX object tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp +[ 11%] Linking CXX executable ../../bin/test_basic_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_iterator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_iterator.dir/test_basic_iterator.cpp.o -o ../../bin/test_basic_iterator -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Built target test_basic_iterator +make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/depend.internal". +Scanning dependencies of target test_find +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 11%] Building CXX object tests/find/CMakeFiles/test_find.dir/test_find.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find.dir/test_find.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, from /build/seqan2-2.4.0+dfsg/tests/bed_io/test_bed_io.cpp:39: @@ -31597,8 +31675,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 11%] Linking CXX executable ../../bin/test_basic_smart_pointer -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_smart_pointer.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/bed_io/test_bed_io.cpp:38: @@ -31618,39 +31694,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_smart_pointer.dir/test_basic_smart_pointer.cpp.o -o ../../bin/test_basic_smart_pointer -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_smart_pointer -make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/depend.internal". -Scanning dependencies of target test_consensus -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/consensus/CMakeFiles/test_consensus.dir/test_consensus.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_consensus.dir/test_consensus.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp -[ 11%] Linking CXX executable ../../bin/test_basic_iterator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_iterator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_iterator.dir/test_basic_iterator.cpp.o -o ../../bin/test_basic_iterator -lrt -lz -lbz2 +[ 11%] Linking CXX executable ../../bin/test_arg_parse_version_check +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_arg_parse_version_check.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_arg_parse_version_check.dir/test_arg_parse_version_check.cpp.o -o ../../bin/test_arg_parse_version_check -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_iterator -make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend +[ 11%] Built target test_arg_parse_version_check +make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend.internal". -Scanning dependencies of target test_consensus_v2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/depend.internal". +Scanning dependencies of target test_gff_io make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build +make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp -[ 11%] Linking CXX executable ../../bin/test_align_simd_global_variable_length -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_variable_length.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -o ../../bin/test_align_simd_global_variable_length -lrt -lz -lbz2 +[ 11%] Building CXX object tests/gff_io/CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -31698,7 +31757,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:61, from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_record.h: In instantiation of 'seqan::BlastMatch::BlastMatch(const TQId&, const TSId&) [with TAlignRow0_ = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >; TAlignRow1_ = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >; TPos_ = unsigned int; TQId_ = seqan::Segment >, seqan::InfixSegment>; TSId_ = seqan::String >; TSAccs_ = std::vector >; TSTaxIds_ = seqan::String >; seqan::BlastMatch::TQId = seqan::Segment >, seqan::InfixSegment>; seqan::BlastMatch::TSId = seqan::String >]': @@ -31742,8 +31800,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 11%] Built target test_align_simd_global_variable_length -make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:37: @@ -31766,16 +31822,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/depend.internal". -Scanning dependencies of target test_find -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/find/CMakeFiles/test_find.dir/test_find.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find.dir/test_find.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: @@ -31832,170 +31878,1012 @@ | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:61, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_record.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TParam = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TParam = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TSource1 = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TSource2 = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1785:50: required from 'typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >; TSpec = seqan::Alloc<>; TSize = int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >&; TSize = int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:145:11: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:514:21: required from 'void SEQAN_TEST_test_blast_write_lowlevel() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:63:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_record.h:378:8: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 378 | struct BlastRecord + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >::BlastRecord(seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::PrefixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::PrefixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::PrefixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::PrefixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:596:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:736:16: required from 'void seqan::writeRecord(seqan::BlastReportFileOut&, const seqan::BlastRecord&) [with TContext = seqan::BlastIOContext<>; TSpecs = {seqan::BlastMatch, seqan::Alloc >, seqan::Tag >, seqan::Gaps, seqan::Alloc >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String >, std::vector, std::allocator >, std::allocator, std::allocator > > >, seqan::String > >, seqan::Segment >, seqan::InfixSegment>, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::__cxx11::basic_string, std::allocator >, unsigned int}; seqan::BlastReportFileOut = seqan::FormattedFile, seqan::Tag, seqan::BlastIOContext<> >]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:52:20: required from 'void _testBlastOutputWriteFile(TFile&, seqan::BlastIOContext&, const TRecords&, const BlastReport&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TRecords = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC; seqan::BlastReport = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:192:30: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:634:21: required from 'void SEQAN_TEST_test_blast_write_report() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:78:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:551:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:736:16: required from 'void seqan::writeRecord(seqan::BlastReportFileOut&, const seqan::BlastRecord&) [with TContext = seqan::BlastIOContext<>; TSpecs = {seqan::BlastMatch, seqan::Alloc >, seqan::Tag >, seqan::Gaps, seqan::Alloc >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String >, std::vector, std::allocator >, std::allocator, std::allocator > > >, seqan::String > >, seqan::Segment >, seqan::InfixSegment>, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::__cxx11::basic_string, std::allocator >, unsigned int}; seqan::BlastReportFileOut = seqan::FormattedFile, seqan::Tag, seqan::BlastIOContext<> >]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:52:20: required from 'void _testBlastOutputWriteFile(TFile&, seqan::BlastIOContext&, const TRecords&, const BlastReport&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TRecords = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC; seqan::BlastReport = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:192:30: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:634:21: required from 'void SEQAN_TEST_test_blast_write_report() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:78:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:305:34: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:305:34: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; TIntegral = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 577 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 577 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder >, seqan::InfixSegment>, void>; TNeedle = seqan::String >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1625:16: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder >, seqan::InfixSegment>, void>; TNeedle = seqan::String >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:427:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 599 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1625:16: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:427:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 599 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:53: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; TIntegral = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:332:42: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:332:42: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:53: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::PrefixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] + 625 | return ModifiedString(host); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::InfixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::InfixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::InfixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&; TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1594:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 625 | return ModifiedString(host); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 625 | return ModifiedString(host); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 117 | ModifiedString(typename Parameter_::Type host) : + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::PrefixSegment>*; TParam = const seqan::Segment >, seqan::PrefixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::PrefixSegment>*; TParam = const seqan::Segment >, seqan::PrefixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::PrefixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; TValue2 = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::PrefixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; TValue2 = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::PrefixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&; TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1594:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::SuffixSegment>*; TParam = const seqan::Segment >, seqan::SuffixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::SuffixSegment>*; TParam = const seqan::Segment >, seqan::SuffixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::SuffixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; TValue2 = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::SuffixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; TValue2 = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>; THasState = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:121:49: required from 'void seqan::createTrie(seqan::Graph >&, TTerminalStateMap&, const TKeywords&) [with TAlphabet = char; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeywords = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:147:15: required from 'void seqan::_createAcTrie(seqan::Pattern >&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:209:18: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; TNeedle2 = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:373:10: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:61, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_record.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TParam = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TParam = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TSource1 = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*; TSource2 = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1785:50: required from 'typename seqan::Size >::Type seqan::resize(seqan::String&, TSize, seqan::Tag) [with TValue = seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >; TSpec = seqan::Alloc<>; TSize = int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1149:18: required from 'typename seqan::Size::Type seqan::resize(T&&, TSize) [with T = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >&; TSize = int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:145:11: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:514:21: required from 'void SEQAN_TEST_test_blast_write_lowlevel() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:63:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_record.h:378:8: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 378 | struct BlastRecord - | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TPos = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:121:49: required from 'void seqan::createTrie(seqan::Graph >&, TTerminalStateMap&, const TKeywords&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeywords = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:147:15: required from 'void seqan::_createAcTrie(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:209:18: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; TNeedle2 = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:373:10: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >::BlastRecord(seqan::BlastRecord, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > >&&)' first required here + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:463:23: required from 'void seqan::_arrayConstructCopyDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TSource1 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TSource2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1023:31: required from 'void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::False) [with TValueSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValueTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1031:31: required from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValueTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1011:31: required from 'static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1056:42: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; typename seqan::Host >::Type = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:269:49: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::PrefixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::PrefixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::PrefixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::PrefixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::PrefixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:596:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:736:16: required from 'void seqan::writeRecord(seqan::BlastReportFileOut&, const seqan::BlastRecord&) [with TContext = seqan::BlastIOContext<>; TSpecs = {seqan::BlastMatch, seqan::Alloc >, seqan::Tag >, seqan::Gaps, seqan::Alloc >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String >, std::vector, std::allocator >, std::allocator, std::allocator > > >, seqan::String > >, seqan::Segment >, seqan::InfixSegment>, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::__cxx11::basic_string, std::allocator >, unsigned int}; seqan::BlastReportFileOut = seqan::FormattedFile, seqan::Tag, seqan::BlastIOContext<> >]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:52:20: required from 'void _testBlastOutputWriteFile(TFile&, seqan::BlastIOContext&, const TRecords&, const BlastReport&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TRecords = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC; seqan::BlastReport = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:192:30: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:634:21: required from 'void SEQAN_TEST_test_blast_write_report() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:78:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, std::char_traits >, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:551:14: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/blast/blast_report_out.h:736:16: required from 'void seqan::writeRecord(seqan::BlastReportFileOut&, const seqan::BlastRecord&) [with TContext = seqan::BlastIOContext<>; TSpecs = {seqan::BlastMatch, seqan::Alloc >, seqan::Tag >, seqan::Gaps, seqan::Alloc >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String >, std::vector, std::allocator >, std::allocator, std::allocator > > >, seqan::String > >, seqan::Segment >, seqan::InfixSegment>, std::vector, std::allocator >, std::allocator, std::allocator > > >, std::__cxx11::basic_string, std::allocator >, unsigned int}; seqan::BlastReportFileOut = seqan::FormattedFile, seqan::Tag, seqan::BlastIOContext<> >]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:52:20: required from 'void _testBlastOutputWriteFile(TFile&, seqan::BlastIOContext&, const TRecords&, const BlastReport&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TRecords = seqan::String, seqan::Alloc<> >, seqan::Tag >, seqan::Gaps, seqan::Alloc<> >, seqan::Tag >, unsigned int, seqan::Segment >, seqan::InfixSegment>, seqan::String > > > >; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC; seqan::BlastReport = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:192:30: required from 'void _testBlastOutputGenerateContent(TFile&, seqan::BlastIOContext&, const TFormat&) [with TFile = std::basic_fstream; TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:497:36: required from 'void _testBlastOutput(seqan::BlastIOContext&, const TFormat&) [with TScore = seqan::Score, seqan::Blosum62_> >; TFormat = seqan::Tag; seqan::BlastProgram p = seqan::BlastProgram::DYNAMIC; seqan::BlastTabularSpec h = seqan::BlastTabularSpec::DYNAMIC]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast_output.h:634:21: required from 'void SEQAN_TEST_test_blast_write_report() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:78:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/blast/test_blast.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:39, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: @@ -32023,30 +32911,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, @@ -32068,51 +32932,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:39, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: @@ -32141,94 +32960,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, @@ -32250,107 +32981,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:305:34: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:305:34: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; TIntegral = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 577 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 577 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' @@ -32419,44 +33049,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -32480,28 +33096,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:370:17: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:334:30: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:163:34: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] - 518 | indexShape(host(pattern)) = pattern.shape; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' - 107 | Shape(Shape const &other): - | ^~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: @@ -32542,6 +33156,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: @@ -32626,156 +33265,93 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:261:42: required from 'void seqan::OverlapInfoComputation_::buildGlobalAlignmentOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:161:9: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole<>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:377:20: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:334:30: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:163:34: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 599 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder >, seqan::InfixSegment>, void>; TNeedle = seqan::String >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1625:16: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder >, seqan::InfixSegment>, void>; TNeedle = seqan::String >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:427:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 599 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:301:30: required from 'seqan::Finder::Finder(THaystack&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:425:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1603:45: required from 'bool seqan::find(TFinder&, const seqan::Pattern >&, seqan::PatternState_ >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:1625:16: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, void>; TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::FindInfix; TFindBeginPatternSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:427:15: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 599 | return container(hostIterator(me)); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_builder.h:376:20: required from 'void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:170:20: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, @@ -32861,104 +33437,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:53: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:64: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = unsigned int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:395:33: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': /build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' /build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' /build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: @@ -33023,155 +33515,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; TIntegral = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:332:42: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:577:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:331:53: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_multiple_bfam.h:332:42: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TAutomaton = seqan::Oracle; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::MultiBfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1354:62: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical_multi_bfam() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1925:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:53: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::__cxx11::basic_stringstream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::__cxx11::basic_stringstream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:90:19: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:40, @@ -33199,33 +33580,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h: In instantiation of 'void seqan::_patternInit(seqan::Pattern >&, TFloat) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TFloat = double; TSpec = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:370:17: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:334:30: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:163:34: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:518:35: warning: implicitly-declared 'constexpr seqan::Shape, seqan::OneGappedShape>& seqan::Shape, seqan::OneGappedShape>::operator=(const seqan::Shape, seqan::OneGappedShape>&)' is deprecated [-Wdeprecated-copy] + 518 | indexShape(host(pattern)) = pattern.shape; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' + 107 | Shape(Shape const &other): + | ^~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -33310,117 +33686,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::PrefixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] - 625 | return ModifiedString(host); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::InfixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::InfixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::InfixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&; TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1594:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 625 | return ModifiedString(host); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:76, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h: In instantiation of 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 625 | return ModifiedString(host); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:44, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 117 | ModifiedString(typename Parameter_::Type host) : - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: @@ -33447,73 +33712,188 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:515:18: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >, seqan::Score > > >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >, seqan::Score > > >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::WeightedConsensusScore >, seqan::Score > >; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:657:36: required from 'void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, bool) [with TProfileGaps = seqan::Gaps >, seqan::Alloc<> >, seqan::Tag >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TConsensusScore = seqan::Score >, seqan::Score > > >; TAlignConfig = seqan::AlignConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1209:36: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus_realign.h:63:16: required from 'void SEQAN_TEST_test_consensus_realign_one_contig_small() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:40:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:39, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:355:16: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:261:42: required from 'void seqan::OverlapInfoComputation_::buildGlobalAlignmentOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:161:9: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = char; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >; TSpec = seqan::Bfam; TNeedle2 = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:102:12: required from 'void Test_OnlineAlg() [with TAlgorithmSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1255:32: required from 'void SEQAN_TEST_test_find_online_BFAM_Trie() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1905:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h: In instantiation of 'typename seqan::Parameter_::Type seqan::container(seqan::Finder&) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Pigeonhole<>; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:969:48: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:377:20: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:334:30: required from 'void seqan::OverlapInfoComputation_::buildAllToAllOverlapInfos(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:163:34: required from 'void seqan::OverlapInfoComputation_::run(std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:160:22: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:599:38: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 599 | return container(hostIterator(me)); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Owner<> >&; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_builder.h:376:20: required from 'void seqan::ConsensusBuilder_::run(TFragmentStore&, const std::vector&) const [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner.h:170:20: required from 'void seqan::ConsensusAligner_::run() [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:141:16: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:64: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = unsigned int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:395:33: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:78:23: required from 'void SEQAN_TEST_test_consensus_consensus_alignment_coordinates() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:298:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: @@ -33594,29 +33974,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:196:25: required from 'void seqan::createSuffixTrie(seqan::Graph >&, TTerminalStateMap&, const TText&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = const seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TText = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_bom.h:161:21: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >; TSpec = seqan::Bfam; TNeedle2 = seqan::String, seqan::Alloc<> >&]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1738:16: required from 'void test_pattern_set_host() [with TPatternSpec = seqan::Bfam]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1868:39: required from 'void SEQAN_TEST_test_pattern_set_host() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1934:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:910:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:1006:37: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' @@ -33642,126 +33999,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::PrefixSegment>*; TParam = const seqan::Segment >, seqan::PrefixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::PrefixSegment>*; TParam = const seqan::Segment >, seqan::PrefixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::PrefixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; TValue2 = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::PrefixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::PrefixSegment>; TValue2 = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::PrefixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::PrefixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::PrefixSegment>&; TNeedle = seqan::Segment >, seqan::PrefixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::PrefixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1590:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::PrefixSegment>::Segment(const seqan::Segment >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::InfixSegment>&; TNeedle = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1594:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::SuffixSegment>*; TParam = const seqan::Segment >, seqan::SuffixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::SuffixSegment>*; TParam = const seqan::Segment >, seqan::SuffixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::SuffixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; TValue2 = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Reference > >::Type = seqan::Segment >, seqan::SuffixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:840:14: required from 'void seqan::setValue(seqan::Holder >&, const TValue2&) [with TValue = seqan::Segment >, seqan::SuffixSegment>; TValue2 = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:254:13: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:118:25: required from 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:625:12: required from 'seqan::ModifiedString > seqan::reverseString(THost&) [with THost = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:212:61: required from 'static void seqan::FindBeginImpl_ >::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>; THasState = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_begin.h:330:65: required from 'void seqan::_findBeginInit(TPattern&, TNeedle&) [with TPattern = seqan::Pattern >, seqan::SuffixSegment>, seqan::Myers<> >; TNeedle = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:558:19: required from 'void seqan::_patternFirstInit(seqan::Pattern >&, TNeedle2&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers; TNeedle2 = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:660:22: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Myers<>; TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_myers_ukkonen.h:452:16: required from 'seqan::Pattern >::Pattern(TNeedle2&&, int) [with TNeedle2 = const seqan::Segment >, seqan::SuffixSegment>&; TNeedle = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::FindInfix; THasState = seqan::True; TFindBeginPatternSpec = seqan::Myers]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1566:50: required from 'void test_find_on_segments_Helper(TString&, const TSegmentOrString&) [with TString = seqan::String >; TSegmentOrString = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1598:35: required from 'void SEQAN_TEST_test_find_on_segments() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1889:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:46, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:41: @@ -33886,39 +34123,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:515:18: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >, seqan::Score > > >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >, seqan::Score > > >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::String >, seqan::Alloc<> >; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreValue2 = int; TScoreSpec = seqan::WeightedConsensusScore >, seqan::Score > >; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:657:36: required from 'void seqan::_readToProfileAlignment(TProfileGaps&, TReadGaps&, const TConsensusScore&, const TAlignConfig&, int&, int&, bool) [with TProfileGaps = seqan::Gaps >, seqan::Alloc<> >, seqan::Tag >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TConsensusScore = seqan::Score >, seqan::Score > > >; TAlignConfig = seqan::AlignConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1209:36: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus_realign.h:63:16: required from 'void SEQAN_TEST_test_consensus_realign_one_contig_small() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:40:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.h:39, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/consensus/test_consensus.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: @@ -33988,91 +34192,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = char; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment >, seqan::InfixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:121:49: required from 'void seqan::createTrie(seqan::Graph >&, TTerminalStateMap&, const TKeywords&) [with TAlphabet = char; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeywords = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:147:15: required from 'void seqan::_createAcTrie(seqan::Pattern >&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:209:18: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; TNeedle2 = seqan::String >, seqan::InfixSegment>, seqan::Alloc<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:373:10: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String >; TFinder = seqan::Finder > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder > >; TNeedle = seqan::String >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:923:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:66:64: required from 'void seqan::_addStringToTrie(seqan::Graph >&, TTerminalStateMap&, const TKeyword&, const TPos&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeyword = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TPos = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_types/graph_impl_trie.h:121:49: required from 'void seqan::createTrie(seqan::Graph >&, TTerminalStateMap&, const TKeywords&) [with TAlphabet = seqan::SimpleType; TCargo = void; TSpec = seqan::Tag; TTerminalStateMap = seqan::String >, seqan::Alloc<> >; TKeywords = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:147:15: required from 'void seqan::_createAcTrie(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:209:18: required from 'void seqan::_reinitPattern(seqan::Pattern >&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:255:19: required from 'void seqan::setHost(seqan::Pattern&, TNeedle2&&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; TNeedle2 = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:373:10: required from 'void seqan::_patternInit(seqan::Pattern >&, TFinder&) [with TNeedle = seqan::String, seqan::Alloc<> >; TFinder = seqan::Finder, seqan::Alloc<> > >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:412:18: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:53: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:463:23: required from 'void seqan::_arrayConstructCopyDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TSource1 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TSource2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1023:31: required from 'void seqan::_arrayConstructCopyPointer(TValueSource*, TValueSource*, TValueTarget*, seqan::False) [with TValueSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValueTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1031:31: required from 'void seqan::arrayConstructCopy(TValueSource*, TValueSource*, TValueTarget*) [with TValueSource = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValueTarget = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1011:31: required from 'static void seqan::AssignString_::assign_(TTarget&, TSource&) [with TTarget = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSource = const seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1056:42: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TSpec = seqan::Tag; typename seqan::Host >::Type = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_ahocorasick.h:269:49: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pex.h:446:13: required from 'bool seqan::find(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> > >; TNeedle = seqan::String, seqan::Alloc<> >; TMultiFinder = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:990:5: required from 'void Test_Approx_EditDist() [with TPatternSpec = seqan::Pex >]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1339:45: required from 'void SEQAN_TEST_test_approx_edit_dist_pex_non_hierarchical() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:1921:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/tests/find/test_find.cpp:54: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/consensus_v2/test_consensus_v2.cpp:40: @@ -34418,98 +34537,6 @@ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_bed_io.dir/test_bed_io.cpp.o -o ../../bin/test_bed_io -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 11%] Built target test_bed_io -make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/depend.internal". -Scanning dependencies of target test_gff_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Building CXX object tests/gff_io/CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.h:353:15: required from 'void SEQAN_TEST_test_store_io_gff_stream_read_record_gff() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/gff_io/test_gff_io.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 11%] Linking CXX executable ../../bin/test_arg_parse -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_arg_parse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o -o ../../bin/test_arg_parse -lrt -lz -lbz2 -[ 11%] Linking CXX executable ../../bin/test_align_simd_global_equal_length -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_equal_length.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -o ../../bin/test_align_simd_global_equal_length -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_arg_parse make -f tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build.make tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_algorithms /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/DependInfo.cmake --color= @@ -34521,8 +34548,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 11%] Building CXX object tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/test_graph_algorithms.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_algorithms.dir/test_graph_algorithms.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_algorithms/test_graph_algorithms.cpp +[ 11%] Linking CXX executable ../../bin/test_arg_parse +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_arg_parse.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_arg_parse.dir/test_arg_parse.cpp.o -o ../../bin/test_arg_parse -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_align_simd_global_equal_length +[ 11%] Built target test_arg_parse make -f tests/graph_align/CMakeFiles/test_graph_align.dir/build.make tests/graph_align/CMakeFiles/test_graph_align.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align/CMakeFiles/test_graph_align.dir/DependInfo.cmake --color= @@ -34534,6 +34564,9 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 11%] Building CXX object tests/graph_align/CMakeFiles/test_graph_align.dir/test_graph_align.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_align.dir/test_graph_align.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_align/test_graph_align.cpp +[ 11%] Linking CXX executable ../../bin/snp_store +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store && /usr/bin/cmake -E cmake_link_script CMakeFiles/snp_store.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/snp_store.dir/snp_store.cpp.o -o ../../bin/snp_store -lrt -lz -lbz2 [ 11%] Linking CXX executable ../../bin/test_bam_io cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bam_io.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_bam_io.dir/test_bam_io.cpp.o -o ../../bin/test_bam_io -lrt -lz -lbz2 @@ -34550,6 +34583,54 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 11%] Building CXX object tests/graph_msa/CMakeFiles/test_graph_msa.dir/test_graph_msa.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_msa.dir/test_graph_msa.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Linking CXX executable ../../bin/test_gff_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_gff_io.dir/link.txt --verbose=1 +[ 12%] Built target snp_store +make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o -o ../../bin/test_gff_io -lrt -lz -lbz2 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend.internal". +Scanning dependencies of target test_graph_types_utils +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_utils.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Built target test_gff_io +make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend.internal". +Scanning dependencies of target test_graph_types_types +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_types.cpp +[ 12%] Linking CXX executable ../../bin/seqcons2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqcons2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqcons2.dir/seqcons.cpp.o CMakeFiles/seqcons2.dir/seqcons_app.cpp.o CMakeFiles/seqcons2.dir/seqcons_options.cpp.o -o ../../bin/seqcons2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Built target seqcons2 +make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend.internal". +Scanning dependencies of target test_graph_types_iterators +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_iterators.cpp +[ 12%] Linking CXX executable ../../bin/s4_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_search.dir/search.cpp.o -o ../../bin/s4_search -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -34580,6 +34661,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/tests/graph_align/test_graph_align.cpp:47: /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': @@ -34605,6 +34687,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ +[ 12%] Built target s4_search In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/tests/graph_align/test_graph_align.cpp:47: /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] @@ -34615,6 +34698,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ +make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend.internal". +Scanning dependencies of target test_graph_types_derived +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_derived.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -34646,6 +34740,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 12%] Linking CXX executable ../../bin/s4_join +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin && /usr/bin/cmake -E cmake_link_script CMakeFiles/s4_join.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/s4_join.dir/join.cpp.o -o ../../bin/s4_join -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:50, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io/bam_sam.h:39, @@ -34989,6 +35086,59 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String > >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String > >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' +/build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:459:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1667 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1679 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1701 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Built target s4_join +make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend.internal". +Scanning dependencies of target test_graph_types_property_map +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_property_map.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -35089,110 +35239,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String > >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String > >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' -/build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_tcoffee.h:459:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1667 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1679 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1701 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/tests/graph_msa/test_graph_msa.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -[ 12%] Linking CXX executable ../../bin/test_gff_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_gff_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_gff_io.dir/test_gff_io.cpp.o -o ../../bin/test_gff_io -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_gff_io -make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend.internal". -Scanning dependencies of target test_graph_types_utils -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_utils.cpp -[ 12%] Linking CXX executable ../../bin/test_graph_algorithms -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_algorithms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_algorithms.dir/test_graph_algorithms.cpp.o -o ../../bin/test_graph_algorithms -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_algorithms -make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend.internal". -Scanning dependencies of target test_graph_types_types -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_types.cpp -[ 12%] Linking CXX executable ../../bin/test_graph_types_utils -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_utils.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o -o ../../bin/test_graph_types_utils -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_types_utils -make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend.internal". -Scanning dependencies of target test_graph_types_iterators -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_iterators.cpp -[ 12%] Linking CXX executable ../../bin/test_consensus -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_consensus.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_consensus.dir/test_consensus.cpp.o -o ../../bin/test_consensus -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_consensus -make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend.internal". -Scanning dependencies of target test_graph_types_derived -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_derived.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_derived.cpp:33: @@ -35254,37 +35300,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = char*]' 129 | operator = (Segment const & source) | ^~~~~~~~ -[ 12%] Linking CXX executable ../../bin/test_graph_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_align.dir/test_graph_align.cpp.o -o ../../bin/test_graph_align -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_align -[ 12%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/param_tabs.cpp -[ 12%] Linking CXX executable ../../bin/test_graph_types_derived -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_derived.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o -o ../../bin/test_graph_types_derived -lrt -lz -lbz2 -[ 12%] Linking CXX executable ../../bin/test_blast -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_blast.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_blast.dir/test_blast.cpp.o -o ../../bin/test_blast -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_types_derived -make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend.internal". -Scanning dependencies of target test_graph_types_property_map -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/graph_types/test_graph_types_property_map.cpp -[ 12%] Linking CXX executable ../../bin/test_consensus_v2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_consensus_v2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o -o ../../bin/test_consensus_v2 -lrt -lz -lbz2 +[ 12%] Linking CXX executable ../../bin/test_graph_types_utils +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_utils.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_utils.dir/test_graph_types_utils.cpp.o -o ../../bin/test_graph_types_utils -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_blast +[ 12%] Built target test_graph_types_utils make -f tests/index/CMakeFiles/test_index_swift.dir/build.make tests/index/CMakeFiles/test_index_swift.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_swift.dir/DependInfo.cmake --color= @@ -35296,11 +35316,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 12%] Building CXX object tests/index/CMakeFiles/test_index_swift.dir/test_index_swift.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_swift.dir/test_index_swift.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp -[ 12%] Linking CXX executable ../../bin/test_graph_types_iterators -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_iterators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o -o ../../bin/test_graph_types_iterators -lrt -lz -lbz2 +[ 12%] Linking CXX executable ../../bin/test_graph_types_derived +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_derived.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_derived.dir/test_graph_types_derived.cpp.o -o ../../bin/test_graph_types_derived -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_consensus_v2 +[ 12%] Built target test_graph_types_derived make -f tests/index/CMakeFiles/test_index_repeats.dir/build.make tests/index/CMakeFiles/test_index_repeats.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_repeats.dir/DependInfo.cmake --color= @@ -35312,8 +35332,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 12%] Building CXX object tests/index/CMakeFiles/test_index_repeats.dir/test_index_repeats.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_repeats.dir/test_index_repeats.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_repeats.cpp +[ 13%] Linking CXX executable ../../bin/test_graph_types_property_map +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_property_map.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o -o ../../bin/test_graph_types_property_map -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_types_iterators +[ 13%] Built target test_graph_types_property_map make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_finder.dir/DependInfo.cmake --color= @@ -35323,19 +35346,11 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/index/CMakeFiles/test_index_finder.dir/test_index_finder.cpp.o +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_finder.dir/test_index_finder.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_finder.dir/test_index_finder.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp -make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/depend.internal". -Scanning dependencies of target test_index_view -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Building CXX object tests/index/CMakeFiles/test_index_view.dir/test_index_view.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_view.dir/test_index_view.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.cpp +[ 13%] Linking CXX executable ../../bin/test_graph_algorithms +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_algorithms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_algorithms.dir/test_graph_algorithms.cpp.o -o ../../bin/test_graph_algorithms -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:1: @@ -35371,6 +35386,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_graph_algorithms +make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/depend.internal". +Scanning dependencies of target test_index_view +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_view.dir/test_index_view.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_view.dir/test_index_view.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:740:41: required from 'void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:28:16: required from 'void SEQAN_TEST_test_index_swift_find_empty_pattern() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:34:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<10> >]' + 143 | Index(Index const &other): + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_repeats.cpp:35: @@ -35408,27 +35457,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:740:41: required from 'void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = seqan::String, seqan::Alloc<> >; TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:28:16: required from 'void SEQAN_TEST_test_index_swift_find_empty_pattern() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:34:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_swift.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram, seqan::UngappedShape<10> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<10> >]' - 143 | Index(Index const &other): - | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -35580,8 +35608,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ -[ 12%] Linking CXX executable ../../bin/test_graph_msa -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_msa.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:220, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h: In instantiation of 'void seqan::clear(seqan::Finder, TSpecFinder>&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag]': @@ -35640,7 +35666,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter > >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA > >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_msa.dir/test_graph_msa.cpp.o -o ../../bin/test_graph_msa -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:220, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h: In instantiation of 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [7]]': @@ -36708,7 +36733,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::Packed<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA, seqan::Packed<> >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ -[ 13%] Linking CXX executable ../../bin/test_graph_types_property_map In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:171, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h: In instantiation of 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [7]; seqan::FinderSTree = const seqan::Tag]': @@ -36757,7 +36781,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_property_map.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:171, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h: In instantiation of 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; seqan::FinderSTree = const seqan::Tag]': @@ -36873,7 +36896,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_property_map.dir/test_graph_types_property_map.cpp.o -o ../../bin/test_graph_types_property_map -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]': @@ -37064,7 +37086,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment > > >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::ConcatenatorManyToOne > > >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -37085,8 +37106,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment, seqan::Alloc<> > > >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::ConcatenatorManyToOne, seqan::Alloc<> > > >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 13%] Built target test_graph_types_property_map -make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -37107,8 +37126,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -37129,8 +37146,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Packed<> >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -37171,20 +37186,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target test_index_vstree -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp -[ 13%] Linking CXX executable ../../bin/test_graph_types_types -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_types.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o -o ../../bin/test_graph_types_types -lrt -lz -lbz2 -[ 13%] Built target test_graph_msa -make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -37241,8 +37242,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment > > >, seqan::PrefixSegment>; TIterator = seqan::Iter > >, seqan::ConcatVirtual<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment > > >, seqan::PrefixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -37411,9 +37410,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::PrefixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Scanning dependencies of target test_index_bifm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -37442,7 +37438,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::PrefixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::PrefixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -37569,8 +37564,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index >, seqan::IndexSa<> >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' 88 | Index(Index const & other) : | ^~~~~ -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp +[ 13%] Linking CXX executable ../../bin/test_graph_types_iterators +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_iterators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_iterators.dir/test_graph_types_iterators.cpp.o -o ../../bin/test_graph_types_iterators -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_graph_types_iterators +make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/depend.internal". +Scanning dependencies of target test_index_vstree +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.cpp:35: @@ -37608,19 +37617,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_graph_types_types -make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/depend.internal". -Scanning dependencies of target test_index_qgram -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp +[ 13%] Linking CXX executable ../../bin/test_index_repeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_repeats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_repeats.dir/test_index_repeats.cpp.o -o ../../bin/test_index_repeats -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:233, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.cpp:38: @@ -37637,6 +37636,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:88:5: note: because 'seqan::Index >, void>, seqan::IndexSa<> >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::ContainerView >, void>; TSpec = void]' 88 | Index(Index const & other) : | ^~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_index_repeats +make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_view.cpp:38: @@ -37799,6 +37805,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' 134 | VertexSA(VertexSA const & other) : | ^~~~~~~~ +Scanning dependencies of target test_index_bifm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -37829,6 +37840,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -37855,22 +37867,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 13%] Linking CXX executable ../../bin/test_index_repeats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_repeats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_repeats.dir/test_index_repeats.cpp.o -o ../../bin/test_index_repeats -lrt -lz -lbz2 +[ 13%] Linking CXX executable ../../bin/test_index_swift +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_swift.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_swift.dir/test_index_swift.cpp.o -o ../../bin/test_index_swift -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_index_repeats -make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend +[ 13%] Built target test_index_swift +make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend.internal". -Scanning dependencies of target test_index_crosscompare_char +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/depend.internal". +Scanning dependencies of target test_index_qgram make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/build +make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: @@ -38070,41 +38082,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: @@ -39055,16 +39032,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 13%] Linking CXX executable ../../bin/test_index_swift -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_swift.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_swift.dir/test_index_swift.cpp.o -o ../../bin/test_index_swift -lrt -lz -lbz2 +[ 13%] Linking CXX executable ../../bin/test_index_view +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_view.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_view.dir/test_index_view.cpp.o -o ../../bin/test_index_view -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_index_swift -make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend +[ 13%] Built target test_index_view +make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend.internal". +Scanning dependencies of target test_index_crosscompare_char +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39090,30 +39073,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram > >; TSource = seqan::Index >, seqan::IndexQGram > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram > >; TValue2 = seqan::Index >, seqan::IndexQGram > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_qgram.h:75:33: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, QGramFindLookup) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::QGramFindLookup = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]]' -/build/seqan2-2.4.0+dfsg/tests/index/test_qgram_index.h:327:5: required from 'void seqan::SEQAN_TEST_testQGramFind() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:62:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram > >& seqan::Index >, seqan::IndexQGram > >::operator=(const seqan::Index >, seqan::IndexQGram > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:91, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index >, seqan::IndexQGram > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::String >; TShapeSpec = seqan::UngappedShape<2>; TSpec = seqan::Tag]' - 278 | Index(Index const &other): - | ^~~~~ -Scanning dependencies of target test_index_crosscompare_char_dfi -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39164,9 +39123,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39217,6 +39173,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39462,43 +39453,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 13%] Linking CXX executable ../../bin/test_graph_types_types +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_types_types.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_types_types.dir/test_graph_types_types.cpp.o -o ../../bin/test_graph_types_types -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39548,6 +39505,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram > >; TSource = seqan::Index >, seqan::IndexQGram > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram > >; TValue2 = seqan::Index >, seqan::IndexQGram > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_qgram.h:75:33: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, QGramFindLookup) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::QGramFindLookup = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]]' +/build/seqan2-2.4.0+dfsg/tests/index/test_qgram_index.h:327:5: required from 'void seqan::SEQAN_TEST_testQGramFind() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:62:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram > >& seqan::Index >, seqan::IndexQGram > >::operator=(const seqan::Index >, seqan::IndexQGram > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:91, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_qgram.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index >, seqan::IndexQGram > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::String >; TShapeSpec = seqan::UngappedShape<2>; TSpec = seqan::Tag]' + 278 | Index(Index const &other): + | ^~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_graph_types_types +make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: @@ -39597,148 +39578,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges; THideEmptyEdges = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:73:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2310:26: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PostorderEmptyEdges; THideEmptyEdges = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PostorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:73:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:88:65: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend.internal". +Scanning dependencies of target test_index_crosscompare_char_dfi +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp +[ 13%] Linking CXX executable ../../bin/test_consensus +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_consensus.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_consensus.dir/test_consensus.cpp.o -o ../../bin/test_consensus -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_consensus +make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/depend.internal". +[ 13%] Linking CXX executable ../../bin/test_graph_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_align.dir/test_graph_align.cpp.o -o ../../bin/test_graph_align -lrt -lz -lbz2 +Scanning dependencies of target test_index_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_base.dir/test_index_base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_base.dir/test_index_base.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -39787,35 +39655,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 13%] Linking CXX executable ../../bin/test_index_view -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_view.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_graph_align +make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -39840,7 +39686,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_view.dir/test_index_view.cpp.o -o ../../bin/test_index_view -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -39889,6 +39734,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target test_index_fm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: @@ -40039,6 +39890,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -40358,32 +40246,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: @@ -40468,44 +40330,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ - char, seqan::Dna_>, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' @@ -40521,64 +40346,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -ngSet > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -40604,58 +40377,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -40708,84 +40429,6 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' @@ -40934,26 +40577,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -40979,12 +40602,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: @@ -41012,113 +40629,6 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_index_view -make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/depend -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' @@ -41217,121 +40727,120 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -Scanning dependencies of target test_index_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_base.dir/test_index_base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_base.dir/test_index_base.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:203:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareCharDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:50:2: required from here +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 125 | data_iterator(other_.data_iterator) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges; THideEmptyEdges = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:73:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2310:26: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PostorderEmptyEdges; THideEmptyEdges = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PostorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:73:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:88:65: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' @@ -41339,79 +40848,489 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:203:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareCharDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:50:2: required from here +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Packed<> >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Packed<> >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:203:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareCharDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:50:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:203:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareCharDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:50:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -41439,661 +41358,797 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment >, seqan::InfixSegment>; T2 = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 18 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Packed<> >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Packed<> >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 15 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:105:33: required from 'void TopDownIndexIteratorTest__GoDown::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:103:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 18 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:65:49: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:129:45: required from 'void seqan::crossIndicesChar() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:196:47: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareChar() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:49:2: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:103:13: required from 'bool testBidirectionalIndex(TBiFMIndex&, TText&, TText&, TPattern&) [with TBiFMIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::BidirectionalIndex > > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TPattern = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:198:35: required from 'void BidirectionalFMIndexTest__SearchInStringSet::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:166:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); @@ -42102,15 +42157,13 @@ 2048 | (_arg1), # _arg1, \ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); | ^~~~~~ @@ -42118,8 +42171,7 @@ 2224 | (_arg1), # _arg1)) { \ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ @@ -42132,6 +42184,33 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:103:13: required from 'bool testBidirectionalIndex(TBiFMIndex&, TText&, TText&, TPattern&) [with TBiFMIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::BidirectionalIndex > > >; TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TPattern = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:198:35: required from 'void BidirectionalFMIndexTest__SearchInStringSet::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:166:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' @@ -42264,6 +42343,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Linking CXX executable ../../bin/test_blast +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_blast.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_blast.dir/test_blast.cpp.o -o ../../bin/test_blast -lrt -lz -lbz2 +[ 13%] Linking CXX executable ../../bin/test_index_qgram +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_qgram.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o -o ../../bin/test_index_qgram -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -42534,6 +42619,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -42642,6 +42728,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Built target test_index_qgram +make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -42723,6 +42813,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -42858,6 +42950,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_blast +Scanning dependencies of target test_index_fm_rank_dictionary +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build +make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -42966,6 +43067,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend.internal". +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43020,6 +43125,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target test_index_crosscompare_dna +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43533,6 +43644,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Linking CXX executable ../../bin/test_index_crosscompare_char_dfi +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_char_dfi.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o -o ../../bin/test_index_crosscompare_char_dfi -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43698,6 +43812,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43753,6 +43868,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Built target test_index_crosscompare_char_dfi +make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43808,6 +43925,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43863,6 +43982,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend.internal". +Scanning dependencies of target test_index_crosscompare_dna_dfi +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43918,9 +44045,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 13%] Linking CXX executable ../../bin/test_find -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find.dir/test_find.cpp.o -o ../../bin/test_find -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_bifm.cpp:35: @@ -43976,39 +44100,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 13%] Linking CXX executable ../../bin/test_index_crosscompare_char_dfi -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_char_dfi.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_char_dfi.dir/test_index_crosscompare_char_dfi.cpp.o -o ../../bin/test_index_crosscompare_char_dfi -lrt -lz -lbz2 -[ 13%] Linking CXX executable ../../bin/test_index_qgram -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_qgram.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_qgram.dir/test_index_qgram.cpp.o -o ../../bin/test_index_qgram -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_find -make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/depend.internal". -[ 13%] Built target test_index_crosscompare_char_dfi -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/DependInfo.cmake --color= -[ 13%] Built target test_index_qgram -make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend.internal". -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend.internal". -Scanning dependencies of target test_index_fm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp +[ 13%] Linking CXX executable ../../bin/test_graph_msa +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_graph_msa.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_graph_msa.dir/test_graph_msa.cpp.o -o ../../bin/test_graph_msa -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -44034,15 +44128,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -Scanning dependencies of target test_index_crosscompare_dna -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o -Scanning dependencies of target test_index_fm_rank_dictionary -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -44068,9 +44153,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_graph_msa +make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Building CXX object tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, @@ -44096,6 +44185,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target test_index_sa_bwtwalk +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, @@ -44121,6 +44213,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, @@ -44196,6 +44326,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, @@ -44326,10 +44493,124 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' @@ -44338,24 +44619,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' @@ -44364,24 +44643,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' @@ -44390,24 +44667,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' @@ -44416,24 +44691,46 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' @@ -44442,24 +44739,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' @@ -44468,24 +44763,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' @@ -44494,24 +44787,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' @@ -44520,24 +44811,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' @@ -44546,291 +44835,175 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' @@ -44839,9 +45012,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -44849,15 +45022,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' @@ -44866,9 +45038,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -44876,15 +45048,74 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:100:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:215:51: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:215:51: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' @@ -44893,25 +45124,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' @@ -44920,360 +45150,107 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::External > >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long long unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -45281,205 +45258,97 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -45487,13 +45356,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, @@ -45501,378 +45382,110 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_rank_dictionary.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:100:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:215:51: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:215:51: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::External > >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long long unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PreorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:101:104: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -45957,6 +45570,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long long unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -46023,6 +45690,102 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -46112,6 +45875,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -46134,6 +45951,102 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -46156,6 +46069,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: @@ -46179,6 +46129,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::External > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::External > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: @@ -46268,374 +46272,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2310:26: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PostorderEmptyEdges; THideEmptyEdges = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PostorderEmptyEdges]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:74:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:106:65: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet, seqan::Alloc<> > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:208:46: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDna() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:52:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:136, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_concat_direct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >*; TParam = const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >*; TParam = const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Packed<> >, seqan::Owner > >, seqan::Tag >; TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; typename seqan::Value::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TValue2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; typename seqan::Reference > >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:786:21: required from 'typename seqan::Fibre, const seqan::Tag >::Type& seqan::getFibre(seqan::Index&, FibreText) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TSpec = seqan::IndexEsa<>; typename seqan::Fibre, const seqan::Tag >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; seqan::FibreText = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:1357:122: required from 'typename seqan::Fibre, const seqan::Tag >::Type& seqan::indexText(seqan::Index&) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TSpec = seqan::IndexEsa<>; typename seqan::Fibre, const seqan::Tag >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:98:5: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_concat_direct.h:81:7: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] - 81 | class StringSet > > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::StringSet, seqan::Packed<> >, seqan::Owner > >::StringSet(const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Packed<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::External > >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::External > >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::External > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::External > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::External > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::External > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TIterator = seqan::ExtStringFwdConstIterator, seqan::External > > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::MMap<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::MMap<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::External > >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' @@ -46644,22 +46288,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' @@ -46668,118 +46313,153 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2310:26: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::PostorderEmptyEdges; THideEmptyEdges = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >; TTraits = seqan::PostorderEmptyEdges]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:74:15: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:106:65: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Packed<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' @@ -46788,9 +46468,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: @@ -46800,11 +46480,12 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' @@ -46812,403 +46493,153 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = SmallWTFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 762 | *cur = Val_; | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, +[ 13%] Linking CXX executable ../../bin/test_align_simd_global_variable_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_variable_length.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' /build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_variable_length.dir/test_align_simd_global_variable_length.cpp.o -o ../../bin/test_align_simd_global_variable_length -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47259,6 +46690,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet, seqan::Alloc<> > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:208:46: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDna() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:52:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47309,6 +46772,70 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:136, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_concat_direct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >*; TParam = const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >*; TParam = const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Packed<> >, seqan::Owner > >, seqan::Tag >; TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; typename seqan::Value::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TValue2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; typename seqan::Reference > >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:786:21: required from 'typename seqan::Fibre, const seqan::Tag >::Type& seqan::getFibre(seqan::Index&, FibreText) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TSpec = seqan::IndexEsa<>; typename seqan::Fibre, const seqan::Tag >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; seqan::FibreText = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_base.h:1357:122: required from 'typename seqan::Fibre, const seqan::Tag >::Type& seqan::indexText(seqan::Index&) [with TText = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >; TSpec = seqan::IndexEsa<>; typename seqan::Fibre, const seqan::Tag >::Type = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:98:5: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_concat_direct.h:81:7: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] + 81 | class StringSet > > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::StringSet, seqan::Packed<> >, seqan::Owner > >::StringSet(const seqan::StringSet, seqan::Packed<> >, seqan::Owner > >&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Packed<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47359,6 +46886,124 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::External > >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::External > >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::External > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::External > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::External > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::External > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TIterator = seqan::ExtStringFwdConstIterator, seqan::External > > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::MMap<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::MMap<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47430,33 +47075,87 @@ | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = PrefixLVFMIndexConfig<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:714:20: required from 'void FibreTest::setUp() [with TIndex = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex > >; TFibreTag = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:709:10: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, @@ -47486,6 +47185,63 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +[ 13%] Linking CXX executable ../../bin/test_consensus_v2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_consensus_v2.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' @@ -47534,6 +47290,117 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_consensus_v2.dir/test_consensus_v2.cpp.o -o ../../bin/test_consensus_v2 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet, seqan::Alloc<> > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Alloc<> > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47584,6 +47451,199 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String, seqan::Packed<> >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index, seqan::Packed<> >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47633,6 +47693,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Built target test_align_simd_global_variable_length +make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_consensus_v2 +make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47682,33 +47753,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet, seqan::Alloc<> > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:208:46: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDna() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:52:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/depend.internal". +Scanning dependencies of target test_index_shapes +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47758,33 +47807,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Packed<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47834,53 +47859,65 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::External > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TIterator = seqan::ExtStringFwdConstIterator, seqan::External > > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::External > >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::External > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::External > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::External > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::External > >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::MMap<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +Scanning dependencies of target test_index_creation +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::External > >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index > >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47930,13 +47967,63 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::MMap<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String > >; TText = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:469:23: required from 'bool seqan::indexCreate(seqan::Index >&) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:103:16: required from 'void IndexTest__OpenSave::runTest() [with SEQAN_TParam = seqan::Index >, seqan::FMIndex<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:101:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -47986,6 +48073,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Linking CXX executable ../../bin/test_align_simd_global_equal_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align_simd_global_equal_length.dir/link.txt --verbose=1 +[ 13%] Linking CXX executable ../../bin/seqan_tcoffee +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee && /usr/bin/cmake -E cmake_link_script CMakeFiles/seqan_tcoffee.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align_simd_global_equal_length.dir/test_align_simd_global_equal_length.cpp.o -o ../../bin/test_align_simd_global_equal_length -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/seqan_tcoffee.dir/seqan_tcoffee.cpp.o -o ../../bin/seqan_tcoffee -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: @@ -48035,6 +48128,478 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_align_simd_global_equal_length +make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/depend.internal". +Scanning dependencies of target test_index_drawing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o +[ 13%] Built target seqan_tcoffee +make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/depend.internal". +Scanning dependencies of target test_find2_index_approx +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>; TText = seqan::StringSet, seqan::Alloc<> > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexEsa<>; TIndexSpec2 = seqan::IndexWotd<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:208:46: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDna() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:52:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Packed<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Packed<> >, seqan::Packed<> >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Packed<> >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Packed<> >, seqan::Packed<> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::Packed<> >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::Packed<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::Packed<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:216:52: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Packed<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Packed<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::External > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TIterator = seqan::ExtStringFwdConstIterator, seqan::External > > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::External > >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::External > >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::External > >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::External > > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::External > >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::External > >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::External > >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::External > >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::External >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:217:54: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::External > >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::External > >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::External > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::External > >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::MMap<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::MMap<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexEsa<> >; TIndex2 = seqan::Index, seqan::MMap<> >, seqan::Owner > >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:105:64: required from 'void seqan::crossSameIndex(TText1&, TText2&) [with TIndexSpec = seqan::IndexEsa<>; TText1 = seqan::StringSet, seqan::Alloc<> > >; TText2 = seqan::StringSet, seqan::MMap<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:191:32: required from 'void seqan::crossStringsDna() [with TIndexSpec = seqan::IndexEsa<>; TStringSpec1 = seqan::Alloc<>; TStringSpec2 = seqan::MMap<>]' +/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:218:50: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaStrings() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:53:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::MMap<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::MMap<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:42: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_char.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -48061,6 +48626,150 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 13%] Linking CXX executable ../../bin/test_index_crosscompare_dna_dfi +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_dna_dfi.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o -o ../../bin/test_index_crosscompare_dna_dfi -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:67:15: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:67:15: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2256:24: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:69:21: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1838 | oldParentDesc = nodeUp(it); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:69:21: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -48087,6 +48796,90 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 13%] Built target test_index_crosscompare_dna_dfi +make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/depend.internal". +Scanning dependencies of target test_find_backtracking +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -48815,6 +49608,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +[ 13%] Linking CXX executable ../../bin/stellar In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -48841,6 +49657,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar && /usr/bin/cmake -E cmake_link_script CMakeFiles/stellar.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/stellar.dir/stellar.cpp.o -o ../../bin/stellar -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -48919,6 +49737,68 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -49023,6 +49903,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -49075,6 +49979,93 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:62:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:54:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::FunctorConvert, char> >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:88:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringViewEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:56:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:62:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:54:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::FunctorConvert, char> >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:88:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringViewEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:56:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -49127,6 +50118,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -49179,6 +50196,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target stellar +make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend.internal". +Scanning dependencies of target test_index_fm_sparse_string +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Building CXX object tests/index/CMakeFiles/test_index_fm_sparse_string.dir/test_index_fm_sparse_string.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm_sparse_string.dir/test_index_fm_sparse_string.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, @@ -49283,881 +50313,344 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 15%] Linking CXX executable ../../bin/test_index_crosscompare_char -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_char.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o -o ../../bin/test_index_crosscompare_char -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Built target test_index_crosscompare_char -make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend.internal". -Scanning dependencies of target test_index_crosscompare_dna_dfi -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Building CXX object tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:70:9: required from 'void seqan::crossBottomUp(TIndex1&, TIndex2&) [with TIterSpec = seqan::TopDown >; TIndex1 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd<> >; TIndex2 = seqan::Index, seqan::Alloc<> > >, seqan::IndexWotd > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:87:66: required from 'void seqan::crossIndex(TText&) [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >; TText = seqan::StringSet, seqan::Alloc<> > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:175:45: required from 'void seqan::crossIndicesDna() [with TIndexSpec1 = seqan::IndexWotd<>; TIndexSpec2 = seqan::IndexWotd >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:229:53: required from 'void seqan::SEQAN_TEST_testIndexCrossCompareDnaDfi() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:53:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_crosscompare.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna_dfi.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 15%] Linking CXX executable ../../bin/test_index_crosscompare_dna_dfi -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_dna_dfi.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_dna_dfi.dir/test_index_crosscompare_dna_dfi.cpp.o -o ../../bin/test_index_crosscompare_dna_dfi -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Built target test_index_crosscompare_dna_dfi -make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend.internal". -Scanning dependencies of target test_index_sa_bwtwalk -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Building CXX object tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/index/test_sa_bwtwalk.h:120:15: required from 'void seqan::SEQAN_TEST_testBWTWalk() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:58:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_sa_bwtwalk.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -[ 15%] Linking CXX executable ../../bin/test_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align.dir/test_align.cpp.o -o ../../bin/test_align -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Built target test_align -make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/depend.internal". -Scanning dependencies of target test_index_shapes -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Building CXX object tests/index/CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_shapes.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 15%] Linking CXX executable ../../bin/test_index_sa_bwtwalk -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_sa_bwtwalk.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o -o ../../bin/test_index_sa_bwtwalk -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Built target test_index_sa_bwtwalk -make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/depend.internal". -Scanning dependencies of target test_index_creation -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 15%] Building CXX object tests/index/CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp -[ 16%] Linking CXX executable ../../bin/test_index_shapes -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_shapes.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o -o ../../bin/test_index_shapes -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_shapes -make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/depend.internal". -Scanning dependencies of target test_index_drawing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/index/CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -[ 16%] Linking CXX executable ../../bin/test_index_fm_rank_dictionary -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_fm_rank_dictionary.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o -o ../../bin/test_index_fm_rank_dictionary -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_fm_rank_dictionary -make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/depend.internal". -Scanning dependencies of target test_find2_index_approx -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/index/CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:67:15: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:67:15: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2256:24: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:69:21: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1838 | oldParentDesc = nodeUp(it); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:69:21: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_drawing.h:101:18: required from 'void seqan::writeRecords(TFile&, seqan::Index >&, seqan::DotDrawing) [with TFile = std::__cxx11::basic_stringstream; TText = seqan::String >; TESASpec = void; seqan::DotDrawing = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:45:17: required from 'void SEQAN_TEST_test_index_drawing_esa_dot() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:80:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_drawing.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:62:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:54:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::FunctorConvert, char> >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:88:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringViewEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:56:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:62:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:54:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::FunctorConvert, char> >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FunctorConvert, char> > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:88:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringViewEsa() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:56:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: @@ -50183,6 +50676,58 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -50200,21 +50745,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: @@ -50279,6 +50809,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 15%] Linking CXX executable ../../bin/test_index_shapes +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_shapes.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_shapes.dir/test_index_shapes.cpp.o -o ../../bin/test_index_shapes -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 15%] Built target test_index_shapes +make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend.internal". +Scanning dependencies of target test_journaled_set +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 15%] Building CXX object tests/journaled_set/CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_set/test_journaled_set.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:42: @@ -50307,7 +50853,7 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); @@ -50316,14 +50862,14 @@ 2048 | (_arg1), # _arg1, \ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); | ^~~~~~ @@ -50331,8 +50877,8 @@ 2224 | (_arg1), # _arg1)) { \ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ @@ -50410,6 +50956,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 15%] Linking CXX executable ../../bin/test_index_drawing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_drawing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o -o ../../bin/test_index_drawing -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: @@ -50494,6 +51043,121 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1348:19: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1349:22: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1348:19: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1349:22: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 15%] Built target test_index_drawing +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend.internal". +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1353:10: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1353:10: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] + 630 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' + 134 | VertexSA(VertexSA const & other) : + | ^~~~~~~~ +Scanning dependencies of target test_journaled_string_tree_find +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: @@ -50510,6 +51174,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 534 | *cb->cur = pool.undefinedValue; | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_find.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: @@ -50653,90 +51319,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: required from 'SEQAN_TEST_test_find2_index_approx_small_test:: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: @@ -50829,1352 +51446,130 @@ | ~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:280:45: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:280:45: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: required from 'seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:626:108: required from 'void seqan::assign(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:651:15: required from 'void seqan::operator<<(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:71:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:440:13: required from 'seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:626:108: required from 'void seqan::assign(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:651:15: required from 'void seqan::operator<<(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:71:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:197:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:476:9: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:617:35: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::StringSet&, const TDistanceTag&, const TParallelTag&) [with unsigned int minErrors = 1; unsigned int maxErrors = 2; TDelegate = SEQAN_TEST_test_find2_index_approx_small_test::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TNeedle = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TDistanceTag = seqan::Tag; TParallelTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:481:15: required from 'void SEQAN_TEST_test_find2_index_approx_small_test() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:109:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1376:22: required from 'bool seqan::operator<<(seqan::Pool&, TSource&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >, seqan::Skew3>, seqan::Filter > >, seqan::Counter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:299:30: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:280:45: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:280:45: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 517 | *cb.cur = item; | ~~~~~~~~^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:81:27: required from 'seqan::Iter >, seqan::VSTree > >::Iter(seqan::Iter >, seqan::VSTree > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:395:15: required from 'void testOptimalSearchScheme(std::array, N>, const TDistanceTag&) [with unsigned int nbrBlocks = 1; unsigned int N = 1; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:420:28: required from 'void SEQAN_TEST_test_find2_index_approx_hamming() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:42:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: required from 'seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:626:108: required from 'void seqan::assign(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:651:15: required from 'void seqan::operator<<(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:71:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 202 | *refNext = *I; | ~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.h:41, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 243 | *cur = *refPrev; | ~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find2_index_approx.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 16%] Linking CXX executable ../../bin/razers3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lrt -lz -lbz2 -[ 16%] Linking CXX executable ../../bin/test_index_drawing -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_drawing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_drawing.dir/test_index_drawing.cpp.o -o ../../bin/test_index_drawing -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_drawing -make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/depend.internal". -Scanning dependencies of target test_find_backtracking -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/index/CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1348:19: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:311:18: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1349:22: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1348:19: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:312:10: required from 'void seqan::goRoot(seqan::Iter >, seqan::VSTree >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1349:22: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:142, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:18: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1353:10: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:377:17: required from 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Preorder; TDfsOrder = seqan::Preorder_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >, seqan::IndexSa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:527:52: required from 'bool seqan::_moveIteratorsDown(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:432:27: required from 'bool seqan::_pushState(seqan::Finder_, seqan::Index, seqan::Backtracking >&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1311:31: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, TDelegate&, const TStage&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TStage = seqan::StageInitial_; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_backtracking.h:1353:10: required from 'void seqan::_find(seqan::Finder_, seqan::Index, seqan::Backtracking >&, seqan::Index&, seqan::Index&, TValue, TDelegate&) [with TText = seqan::String >; TTextIndexSpec = seqan::IndexSa<>; TPattern = seqan::StringSet > >; TPatternIndexSpec = seqan::IndexSa<>; TDistance = seqan::Tag; TSpec = seqan::Tag; TValue = int; TDelegate = FinderTester >, seqan::IndexSa<> >, seqan::Index > >, seqan::IndexSa<> >, seqan::Backtracking > >]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.h:210:10: required from 'void SEQAN_TEST_test_find_backtracking_multiple_hamming_banana_vs_ada_ana() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:45:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:630:20: warning: implicitly-declared 'constexpr seqan::VertexSA& seqan::VertexSA::operator=(const seqan::VertexSA&)' is deprecated [-Wdeprecated-copy] - 630 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_sa_stree.h:134:5: note: because 'seqan::VertexSA' has user-provided 'seqan::VertexSA::VertexSA(const seqan::VertexSA&) [with TSize = unsigned int; TAlphabet = char]' - 134 | VertexSA(VertexSA const & other) : - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target razers3 -make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend.internal". -Scanning dependencies of target test_index_fm_sparse_string -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/index/CMakeFiles/test_index_fm_sparse_string.dir/test_index_fm_sparse_string.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_index_fm_sparse_string.dir/test_index_fm_sparse_string.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, @@ -52201,6 +51596,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, @@ -52307,6 +51726,54 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': @@ -52515,6 +51982,54 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:440:13: required from 'seqan::Pipe& seqan::Pipe::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:626:108: required from 'void seqan::assign(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:651:15: required from 'void seqan::operator<<(seqan::String&, seqan::Pipe&) [with TValue = unsigned int; TStringSpec = seqan::Alloc<>; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:71:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:197:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': @@ -52567,6 +52082,106 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': @@ -52643,8 +52258,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 16%] Linking CXX executable ../../bin/test_index_vstree -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_vstree.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, @@ -52697,7 +52310,159 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o -o ../../bin/test_index_vstree -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +[ 15%] Linking CXX executable ../../bin/test_find +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find.dir/test_find.cpp.o -o ../../bin/test_find -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, @@ -52752,6 +52517,105 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Tag >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:109:21: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': @@ -52802,64 +52666,180 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1376:22: required from 'bool seqan::operator<<(seqan::Pool&, TSource&) [with TValue = seqan::Pair >; TSpec = seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >, seqan::Skew3>, seqan::Filter > >, seqan::Counter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:299:30: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:69:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String >; TObject = seqan::String >; TAlgSpec = seqan::Skew3]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:191:33: required from 'void seqan::SEQAN_TEST_testIndexCreation() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:59:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_vstree -make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend +[ 15%] Built target test_find +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend.internal". -Scanning dependencies of target test_journaled_set +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend.internal". +Scanning dependencies of target test_journaled_string_tree_traverser make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/build +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/journaled_set/CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_set/test_journaled_set.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm_sparse_string.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String, seqan::Packed<> >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -[ 16%] Linking CXX executable ../../bin/test_index_fm_sparse_string +[ 15%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp +[ 15%] Linking CXX executable ../../bin/test_index_fm_sparse_string cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_fm_sparse_string.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_fm_sparse_string.dir/test_index_fm_sparse_string.cpp.o -o ../../bin/test_index_fm_sparse_string -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 4, seqan::Tag >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, 5, seqan::Tag >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:445:22: required from 'bool seqan::indexCreate(seqan::Index >&, FibreSALF) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = void; TConfig = seqan::FMIndexConfig; seqan::FibreSALF = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::ModifiedString, seqan::Alloc<> >, seqan::Tag >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Tag >, seqan::FMIndex<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:75:40: required from 'void seqan::SEQAN_TEST_testIndexModifiedStringReverseFM() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:55:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::Tag >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::Tag >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.h:117:16: required from 'void seqan::SEQAN_TEST_testIssue519() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 15%] Built target test_index_fm_sparse_string +make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend.internal". +Scanning dependencies of target test_delta_map +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -52887,11 +52867,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_fm_sparse_string -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake --color= +[ 15%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -52920,8 +52897,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/journaled_set/test_journaled_set.cpp:36: @@ -52941,10 +52916,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target test_journaled_string_tree_find -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/journaled_set/test_journaled_set.cpp:35: @@ -52965,8 +52936,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 16%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_find.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/journaled_set/test_journaled_set.cpp:36: @@ -53019,32 +52988,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] - 102 | data_iterator = TIterator(); - | ^~~~~~~~~~~~~ -[ 16%] Linking CXX executable ../../bin/test_index_finder -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_finder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_finder.dir/test_index_finder.cpp.o -o ../../bin/test_index_finder -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_index_finder -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend.internal". -Scanning dependencies of target test_journaled_string_tree_traverser -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -53070,8 +53013,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 16%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -53333,22 +53274,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(seqan::JstTraversalNode, seqan::Alloc<> > > >&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 16%] Linking CXX executable ../../bin/test_journaled_set -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_set.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o -o ../../bin/test_journaled_set -lrt -lz -lbz2 +[ 16%] Linking CXX executable ../../bin/test_index_crosscompare_char +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_char.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_char.dir/test_index_crosscompare_char.cpp.o -o ../../bin/test_index_crosscompare_char -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Built target test_journaled_set -make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend +[ 16%] Built target test_index_crosscompare_char +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend.internal". -Scanning dependencies of target test_delta_map +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend.internal". +Scanning dependencies of target test_journaled_string_tree make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 16%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp +[ 16%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp +[ 16%] Linking CXX executable ../../bin/test_index_sa_bwtwalk +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_sa_bwtwalk.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_sa_bwtwalk.dir/test_index_sa_bwtwalk.cpp.o -o ../../bin/test_index_sa_bwtwalk -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 16%] Built target test_index_sa_bwtwalk +make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend.internal". +Scanning dependencies of target test_basic_observable +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 16%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:79, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: @@ -53382,6 +53339,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry::TDeltaPos, seqan::DeltaMapEntry::TDeltaRecord, const TCoverage&, seqan::DeltaEndType) [with TRefPos = unsigned int; TStorePos = unsigned int; seqan::DeltaMapEntry::TDeltaPos = unsigned int; seqan::DeltaMapEntry::TDeltaRecord = seqan::Pair >; seqan::DeltaMapEntry::TCoverage = seqan::String >]': +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.h:114:5: required from 'void SEQAN_TEST_test_delta_map_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:115:29: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 115 | deltaTypeEnd(endType) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:78, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: @@ -53448,6 +53420,63 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -53471,6 +53500,50 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1410:54: required from 'void seqan::insertValue(seqan::String&, TPosition, const TValue&, seqan::Tag) [with TTargetValue = seqan::DeltaMapEntry; TTargetSpec = seqan::Alloc<>; TPosition = int; TValue = seqan::DeltaMapEntry; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1010:16: required from 'void seqan::insertValue(T&&, TPosition, TValue&&) [with T = seqan::String, seqan::Alloc<> >&; TPosition = int; TValue = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:506:16: required from 'void seqan::impl::insert(const seqan::Iter >&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TTag&) [with TDeltaMap = seqan::DeltaMap >; TDeltaPos = int; TDeltaValue = seqan::SimpleType; TCoverage = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:798:17: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = TestDeltaMapConfig; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = seqan::SimpleType; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.h:108:11: required from 'void SEQAN_TEST_test_delta_map_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 86 | class DeltaMapEntry + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1396:33: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(const seqan::DeltaMapEntry&)' first required here + 1396 | typename Value::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: @@ -53495,6 +53568,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:830:18: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(const seqan::JstTraversalNode, seqan::Alloc<> > > >&)' first required here 830 | auto child = *parentPtr; | ^~~~~ +[ 16%] Linking CXX executable ../../bin/test_journaled_set +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_set.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_set.dir/test_journaled_set.cpp.o -o ../../bin/test_journaled_set -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:38: @@ -53533,6 +53609,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 16%] Built target test_journaled_set +[ 16%] Building CXX object apps/razers3/CMakeFiles/razers3.dir/param_tabs.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"3.5.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/razers3.dir/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers3/param_tabs.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:76, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: @@ -53573,6 +53653,34 @@ 163 | String & operator =(String const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::DeltaMapEntry*; TSource1 = seqan::DeltaMapEntry*; TSource2 = seqan::DeltaMapEntry*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: required from 'typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_alloc.h:123:16: required from 'seqan::String >::String(const seqan::String >&) [with TValue = seqan::DeltaMapEntry; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:110:7: required from 'void SEQAN_TEST_test_delta_map_iterator() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:68:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 86 | class DeltaMapEntry + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.h:43, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree_traverser.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': @@ -53655,17 +53763,17 @@ 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry::TDeltaPos, seqan::DeltaMapEntry::TDeltaRecord, const TCoverage&, seqan::DeltaEndType) [with TRefPos = unsigned int; TStorePos = unsigned int; seqan::DeltaMapEntry::TDeltaPos = unsigned int; seqan::DeltaMapEntry::TDeltaRecord = seqan::Pair >; seqan::DeltaMapEntry::TCoverage = seqan::String >]': -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.h:114:5: required from 'void SEQAN_TEST_test_delta_map_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:150:5: required from 'void SEQAN_TEST_test_journaled_string_tree_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:47:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:115:29: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] 115 | deltaTypeEnd(endType) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ @@ -53675,8 +53783,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -53687,27 +53795,24 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 17%] Linking CXX executable ../../bin/test_index_fm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_fm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o -o ../../bin/test_index_fm -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -53719,19 +53824,19 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -53744,115 +53849,44 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1410:54: required from 'void seqan::insertValue(seqan::String&, TPosition, const TValue&, seqan::Tag) [with TTargetValue = seqan::DeltaMapEntry; TTargetSpec = seqan::Alloc<>; TPosition = int; TValue = seqan::DeltaMapEntry; TExpand = seqan::TagGenerous_]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1010:16: required from 'void seqan::insertValue(T&&, TPosition, TValue&&) [with T = seqan::String, seqan::Alloc<> >&; TPosition = int; TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:506:16: required from 'void seqan::impl::insert(const seqan::Iter >&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TTag&) [with TDeltaMap = seqan::DeltaMap >; TDeltaPos = int; TDeltaValue = seqan::SimpleType; TCoverage = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:798:17: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = TestDeltaMapConfig; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = seqan::SimpleType; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.h:108:11: required from 'void SEQAN_TEST_test_delta_map_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:58:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:506:16: required from 'void seqan::impl::insert(const seqan::Iter >&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TTag&) [with TDeltaMap = seqan::DeltaMap, seqan::Alloc<> > >, seqan::Tag >; TDeltaPos = int; TDeltaValue = char; TCoverage = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:798:17: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = char; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_impl.h:619:11: required from 'typename seqan::EnableIf >, void>::Type seqan::insert(seqan::JournaledStringTree&, TPos, const TValue&, const TIds&, TDeltaType) [with TSequence = seqan::String, seqan::Alloc<> >; TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TPos = int; TValue = char; TIds = seqan::String >; TDeltaType = seqan::Tag; typename seqan::EnableIf >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:142:11: required from 'void SEQAN_TEST_test_journaled_string_tree_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:47:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] 86 | class DeltaMapEntry | ^~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1396:33: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(const seqan::DeltaMapEntry&)' first required here 1396 | typename Value::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_store.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::DeltaMapEntry*; TSource1 = seqan::DeltaMapEntry*; TSource2 = seqan::DeltaMapEntry*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: required from 'typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_alloc.h:123:16: required from 'seqan::String >::String(const seqan::String >&) [with TValue = seqan::DeltaMapEntry; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:110:7: required from 'void SEQAN_TEST_test_delta_map_iterator() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:68:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 86 | class DeltaMapEntry - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_delta_map.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 17%] Built target test_index_fm -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend.internal". -Scanning dependencies of target test_journaled_string_tree -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 17%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry::TDeltaPos, seqan::DeltaMapEntry::TDeltaRecord, const TCoverage&, seqan::DeltaEndType) [with TRefPos = unsigned int; TStorePos = unsigned int; seqan::DeltaMapEntry::TDeltaPos = unsigned int; seqan::DeltaMapEntry::TDeltaRecord = seqan::Pair >; seqan::DeltaMapEntry::TCoverage = seqan::String >]': -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:150:5: required from 'void SEQAN_TEST_test_journaled_string_tree_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:47:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:115:29: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 115 | deltaTypeEnd(endType) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -53862,14 +53896,16 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:46, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -53879,8 +53915,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -53891,20 +53927,23 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:46, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -53916,43 +53955,15 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, + from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1410:54: required from 'void seqan::insertValue(seqan::String&, TPosition, const TValue&, seqan::Tag) [with TTargetValue = seqan::DeltaMapEntry; TTargetSpec = seqan::Alloc<>; TPosition = int; TValue = seqan::DeltaMapEntry; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1010:16: required from 'void seqan::insertValue(T&&, TPosition, TValue&&) [with T = seqan::String, seqan::Alloc<> >&; TPosition = int; TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:506:16: required from 'void seqan::impl::insert(const seqan::Iter >&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TTag&) [with TDeltaMap = seqan::DeltaMap, seqan::Alloc<> > >, seqan::Tag >; TDeltaPos = int; TDeltaValue = char; TCoverage = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:798:17: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = char; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_impl.h:619:11: required from 'typename seqan::EnableIf >, void>::Type seqan::insert(seqan::JournaledStringTree&, TPos, const TValue&, const TIds&, TDeltaType) [with TSequence = seqan::String, seqan::Alloc<> >; TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TPos = int; TValue = char; TIds = seqan::String >; TDeltaType = seqan::Tag; typename seqan::EnableIf >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:142:11: required from 'void SEQAN_TEST_test_journaled_string_tree_insert() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:47:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 86 | class DeltaMapEntry - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1396:33: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(const seqan::DeltaMapEntry&)' first required here - 1396 | typename Value::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value - | ^~~~~~~~~ -[ 18%] Linking CXX executable ../../bin/test_journaled_string_tree_find -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree_find.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o -o ../../bin/test_journaled_string_tree_find -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_journaled_string_tree.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::DeltaMapEntry*; TSource1 = seqan::DeltaMapEntry*; TSource2 = seqan::DeltaMapEntry*]' @@ -53978,40 +53989,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry&&)' first required here 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Linking CXX executable ../../bin/test_journaled_string_tree_traverser -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree_traverser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o -o ../../bin/test_journaled_string_tree_traverser -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 18%] Built target test_journaled_string_tree_find -make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend.internal". -[ 18%] Built target test_journaled_string_tree_traverser make -f tests/map/CMakeFiles/test_map.dir/build.make tests/map/CMakeFiles/test_map.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/map /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/test_map.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/test_map.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/test_map.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/test_map.dir/depend.internal". -Scanning dependencies of target test_basic_observable -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build Scanning dependencies of target test_map make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/map/CMakeFiles/test_map.dir/build.make tests/map/CMakeFiles/test_map.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 18%] Building CXX object tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp -[ 18%] Building CXX object tests/map/CMakeFiles/test_map.dir/test_map.cpp.o +[ 16%] Building CXX object tests/map/CMakeFiles/test_map.dir/test_map.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_map.dir/test_map.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/map/test_map.cpp -[ 19%] Linking CXX executable ../../bin/test_delta_map -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_delta_map.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o -o ../../bin/test_delta_map -lrt -lz -lbz2 +[ 16%] Linking CXX executable ../../bin/test_basic_observable +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_observable.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o -o ../../bin/test_basic_observable -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_delta_map +[ 16%] Built target test_basic_observable make -f tests/misc/CMakeFiles/test_misc.dir/build.make tests/misc/CMakeFiles/test_misc.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/misc /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc/CMakeFiles/test_misc.dir/DependInfo.cmake --color= @@ -54021,27 +54014,11 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/misc/CMakeFiles/test_misc.dir/build.make tests/misc/CMakeFiles/test_misc.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/misc/CMakeFiles/test_misc.dir/test_misc.cpp.o +[ 16%] Building CXX object tests/misc/CMakeFiles/test_misc.dir/test_misc.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_misc.dir/test_misc.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/misc/test_misc.cpp -[ 19%] Linking CXX executable ../../bin/test_find2_index_approx -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find2_index_approx.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o -o ../../bin/test_find2_index_approx -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Linking CXX executable ../../bin/test_index_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_base.dir/link.txt --verbose=1 -[ 19%] Built target test_find2_index_approx -make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_base.dir/test_index_base.cpp.o -o ../../bin/test_index_base -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/depend.internal". -Scanning dependencies of target test_modifier -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/modifier/CMakeFiles/test_modifier.dir/test_modifier.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_modifier.dir/test_modifier.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp +[ 17%] Linking CXX executable ../../bin/test_delta_map +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_delta_map.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_delta_map.dir/test_delta_map.cpp.o -o ../../bin/test_delta_map -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/tests/misc/test_misc.cpp:50: /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = double]': /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = double]' @@ -54158,6 +54135,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/tests/misc/test_misc.cpp:50: /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = int]': /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = int]' @@ -54188,11 +54166,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -[ 19%] Linking CXX executable ../../bin/test_index_crosscompare_dna -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_dna.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o -o ../../bin/test_index_crosscompare_dna -lrt -lz -lbz2 +[ 17%] Built target test_delta_map +make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/depend.internal". +Scanning dependencies of target test_modifier +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 17%] Building CXX object tests/modifier/CMakeFiles/test_modifier.dir/test_modifier.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_modifier.dir/test_modifier.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp +[ 17%] Linking CXX executable ../../bin/test_journaled_string_tree +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o -o ../../bin/test_journaled_string_tree -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_base.h:40, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:38: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_find_backtracking.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_index_base +[ 17%] Built target test_journaled_string_tree make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/DependInfo.cmake --color= @@ -54202,41 +54208,22 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/test_modifier_cyclic_shape.cpp.o +[ 17%] Building CXX object tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/test_modifier_cyclic_shape.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_modifier_cyclic_shape.dir/test_modifier_cyclic_shape.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape/test_modifier_cyclic_shape.cpp -[ 19%] Linking CXX executable ../../bin/test_index_bifm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_bifm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o -o ../../bin/test_index_bifm -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:46, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 17%] Linking CXX executable ../../bin/test_journaled_string_tree_traverser +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree_traverser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree_traverser.dir/test_journaled_string_tree_traverser.cpp.o -o ../../bin/test_journaled_string_tree_traverser -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 17%] Built target test_journaled_string_tree_traverser +make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend.internal". +Scanning dependencies of target test_multiple_translation_units +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:40: /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h: In instantiation of 'void SEQAN_TEST_test_modifier_modified_string_construct() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:105:5: required from here @@ -54257,6 +54244,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 17%] Building CXX object tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units.cpp In file included from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:40: /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h: In instantiation of 'void SEQAN_TEST_test_modifier_modified_string_cascade() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:108:5: required from here @@ -54277,6 +54266,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = void; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 18%] Linking CXX executable ../../bin/test_journaled_string_tree_find +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree_find.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:40: /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h: In instantiation of 'void SEQAN_TEST_test_modifier_modified_string_mod_view_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:114:5: required from here @@ -54315,7 +54306,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TFunctor = LowerFunctor; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree_find.dir/test_journaled_string_tree_find.cpp.o -o ../../bin/test_journaled_string_tree_find -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:42: /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string_padding.h: In instantiation of 'void SEQAN_TEST_test_modified_string_padding_defect_2190() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:133:5: required from here @@ -54336,64 +54327,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 19%] Built target test_index_crosscompare_dna -make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:48, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:46, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:45, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.h:41, - from /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree/test_basic_observable.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -54647,6 +54580,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -54665,6 +54599,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 18%] Built target test_journaled_string_tree_find +make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -54683,6 +54623,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target test_parallel +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Building CXX object tests/parallel/CMakeFiles/test_parallel.dir/test_parallel.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_parallel.dir/test_parallel.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/parallel/test_parallel.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -54702,135 +54648,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -In member function 'seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; unsigned int m = 3; TPack = seqan::Tag]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::Source<> >, seqan::Caster >, seqan::Sampler<3> >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:203:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 203 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::Source<> >, seqan::Caster >, seqan::Sampler<3> >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 3 to object 'seqan::Tuple >::i' with size 3 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:320:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_view_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:114:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target test_multiple_translation_units -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h: In instantiation of 'typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:205:36: required from 'typename seqan::Parameter_::Type seqan::cargo(const seqan::ModifiedString >&) [with THost = seqan::String >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:299:24: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Size > >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModPos >, seqan::InfixSegment> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:371:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_pos() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:116:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 365 | return _object; - | ^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:609:22: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:320:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_view_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:114:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; T2 = char [3]]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:447:9: required from 'void SEQAN_TEST_test_modifier_modified_string_reverse_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:120:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape/test_modifier_cyclic_shape.cpp:36: /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape/test_modifier_cyclic_shape.h: In instantiation of 'seqan::String::Type> test_iterator(TString&, const seqan::CyclicShape&) [with TString = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::GappedShape >; typename seqan::Value::Type = char]': /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape/test_modifier_cyclic_shape.h:195:33: required from 'void SEQAN_TEST_test_modifier_cyclic_shape_iterator_generic_infix_charstring() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' @@ -54854,6 +54671,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:214:53: note: initializing argument 1 of 'seqan::ModifiedString > >::ModifiedString(typename seqan::Parameter_::Type, const TCyclicShape&) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::GappedShape >; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>; seqan::ModifiedString > >::TCyclicShape = seqan::CyclicShape > >]' 214 | ModifiedString(typename Parameter_::Type host, TCyclicShape const & shape) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:98:7: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:320:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_view_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:114:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -55027,6 +54865,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' 203 | CyclicShape(CyclicShape const & other) : | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h: In instantiation of 'typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:205:36: required from 'typename seqan::Parameter_::Type seqan::cargo(const seqan::ModifiedString >&) [with THost = seqan::String >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_position.h:299:24: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TPositions = seqan::Segment >, seqan::InfixSegment>; typename seqan::Size > >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModPos >, seqan::InfixSegment> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::ModPos >, seqan::InfixSegment> > >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:371:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_pos() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:116:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 365 | return _object; + | ^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape/test_modifier_cyclic_shape.cpp:35: @@ -55184,24 +55046,74 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:288:5: note: because 'seqan::CyclicShape >, 0> >' has user-provided 'seqan::CyclicShape >, RightOffset> >::CyclicShape(const seqan::CyclicShape >, RightOffset> >&) [with unsigned int LeftOffset = 1; unsigned int RightOffset = 0; int P00 = 1; int P01 = 0; int P02 = 0; int P03 = 0; int P04 = 0; int P05 = 0; int P06 = 0; int P07 = 0; int P08 = 0; int P09 = 0; int P10 = 0; int P11 = 0; int P12 = 0; int P13 = 0; int P14 = 0; int P15 = 0; int P16 = 0; int P17 = 0; int P18 = 0; int P19 = 0]' 288 | CyclicShape(CyclicShape const &) | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:609:22: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:320:9: required from 'void SEQAN_TEST_test_modifier_modified_string_mod_view_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:114:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:663:20: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::end(seqan::ModifiedString&, seqan::Tag) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::ModView; TTagSpec = seqan::Rooted_; typename seqan::Iterator, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_reverse.h:458:102: required from 'typename seqan::Iterator >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString >&, seqan::Tag) [with THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TTagSpec = seqan::Rooted_; typename seqan::Iterator >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::InfixSegment>, seqan::AdaptorIterator > >, seqan::ModView >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:946:71: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::ModifiedString >, seqan::InfixSegment>, seqan::ModView >, seqan::Tag >; T2 = char [3]]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier_string.h:447:9: required from 'void SEQAN_TEST_test_modifier_modified_string_reverse_segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:120:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/tests/modifier/test_modifier.cpp:33: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 18%] Linking CXX executable ../../bin/test_map +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_map.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_map.dir/test_map.cpp.o -o ../../bin/test_map -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_index_bifm -make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/depend.internal". -[ 19%] Linking CXX executable ../../bin/test_basic_observable -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_basic_observable.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_basic_observable.dir/test_basic_observable.cpp.o -o ../../bin/test_basic_observable -lrt -lz -lbz2 -Scanning dependencies of target test_parallel -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/parallel/CMakeFiles/test_parallel.dir/test_parallel.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_parallel.dir/test_parallel.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/parallel/test_parallel.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_basic_observable +[ 18%] Built target test_map make -f tests/parse_lm/CMakeFiles/test_parse_lm.dir/build.make tests/parse_lm/CMakeFiles/test_parse_lm.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/parse_lm /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm/CMakeFiles/test_parse_lm.dir/DependInfo.cmake --color= @@ -55211,56 +55123,23 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/parse_lm/CMakeFiles/test_parse_lm.dir/build.make tests/parse_lm/CMakeFiles/test_parse_lm.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/parse_lm/CMakeFiles/test_parse_lm.dir/test_parse_lm.cpp.o +[ 18%] Building CXX object tests/parse_lm/CMakeFiles/test_parse_lm.dir/test_parse_lm.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_parse_lm.dir/test_parse_lm.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/parse_lm/test_parse_lm.cpp -[ 19%] Linking CXX executable ../../bin/test_find_backtracking -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find_backtracking.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o -o ../../bin/test_find_backtracking -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_find_backtracking -make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/depend.internal". -Scanning dependencies of target test_pipe -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/pipe/CMakeFiles/test_pipe.dir/test_pipe.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_pipe.dir/test_pipe.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp -[ 19%] Linking CXX executable ../../bin/test_journaled_string_tree -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_journaled_string_tree.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_journaled_string_tree.dir/test_journaled_string_tree.cpp.o -o ../../bin/test_journaled_string_tree -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_journaled_string_tree -make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/depend.internal". -Scanning dependencies of target test_platform -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/platform/CMakeFiles/test_platform.dir/test_platform.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_platform.dir/test_platform.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/platform/test_platform.cpp -[ 19%] Linking CXX executable ../../bin/test_map -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_map.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_map.dir/test_map.cpp.o -o ../../bin/test_map -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_map -make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/depend.internal". -Scanning dependencies of target test_random -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/random/CMakeFiles/test_random.dir/test_random.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_random.dir/test_random.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/random/test_random.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:36: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, @@ -55302,6 +55181,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 18%] Linking CXX executable ../../bin/test_modifier_cyclic_shape +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_modifier_cyclic_shape.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_modifier_cyclic_shape.dir/test_modifier_cyclic_shape.cpp.o -o ../../bin/test_modifier_cyclic_shape -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Built target test_modifier_cyclic_shape +make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/depend.internal". +Scanning dependencies of target test_pipe +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Building CXX object tests/pipe/CMakeFiles/test_pipe.dir/test_pipe.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_pipe.dir/test_pipe.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -55378,9 +55273,69 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 19%] Linking CXX executable ../../bin/test_modifier_cyclic_shape -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_modifier_cyclic_shape.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_modifier_cyclic_shape.dir/test_modifier_cyclic_shape.cpp.o -o ../../bin/test_modifier_cyclic_shape -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:37: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ +[ 18%] Linking CXX executable ../../bin/test_index_fm_rank_dictionary +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_fm_rank_dictionary.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_fm_rank_dictionary.dir/test_index_fm_rank_dictionary.cpp.o -o ../../bin/test_index_fm_rank_dictionary -lrt -lz -lbz2 +[ 18%] Linking CXX executable ../../bin/test_misc +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_misc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_misc.dir/test_misc.cpp.o -o ../../bin/test_misc -lrt -lz -lbz2 +[ 18%] Linking CXX executable ../../bin/test_find2_index_approx +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find2_index_approx.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Built target test_misc +make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find2_index_approx.dir/test_find2_index_approx.cpp.o -o ../../bin/test_find2_index_approx -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/depend.internal". +Scanning dependencies of target test_platform +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Building CXX object tests/platform/CMakeFiles/test_platform.dir/test_platform.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_platform.dir/test_platform.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/platform/test_platform.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Built target test_index_fm_rank_dictionary +make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Built target test_find2_index_approx +make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/depend +Scanning dependencies of target test_random +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/DependInfo.cmake --color= +make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Building CXX object tests/random/CMakeFiles/test_random.dir/test_random.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_random.dir/test_random.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/random/test_random.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/depend.internal". +Scanning dependencies of target test_realign +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/realign/CMakeFiles/test_realign.dir/test_realign.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_realign.dir/test_realign.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, @@ -55418,35 +55373,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 19%] Linking CXX executable ../../bin/test_platform -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_platform.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_platform.dir/test_platform.cpp.o -o ../../bin/test_platform -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_modifier_cyclic_shape -make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/DependInfo.cmake --color= -[ 19%] Built target test_platform -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/depend.internal". -make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend.internal". -Scanning dependencies of target test_reduced_aminoacid -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Building CXX object tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp -Scanning dependencies of target test_realign -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object tests/realign/CMakeFiles/test_realign.dir/test_realign.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_realign.dir/test_realign.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -55500,21 +55426,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: -In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', - inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 470 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -55536,9 +55447,102 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 20%] Linking CXX executable ../../bin/test_random +[ 19%] Linking CXX executable ../../bin/test_platform +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_platform.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_platform.dir/test_platform.cpp.o -o ../../bin/test_platform -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_platform +make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/DependInfo.cmake --color= +[ 19%] Linking CXX executable ../../bin/test_find_backtracking +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find_backtracking.dir/link.txt --verbose=1 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend.internal". +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find_backtracking.dir/test_find_backtracking.cpp.o -o ../../bin/test_find_backtracking -lrt -lz -lbz2 +Scanning dependencies of target test_reduced_aminoacid +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_find_backtracking +make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/depend.internal". +Scanning dependencies of target test_rna_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/rna_io/CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp +[ 19%] Linking CXX executable ../../bin/test_parallel +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parallel.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_parallel.dir/test_parallel.cpp.o -o ../../bin/test_parallel -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_parallel +make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/depend.internal". +[ 19%] Linking CXX executable ../../bin/test_parse_lm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parse_lm.dir/link.txt --verbose=1 +Scanning dependencies of target test_roi_io +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_parse_lm.dir/test_parse_lm.cpp.o -o ../../bin/test_parse_lm -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/roi_io/CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp +[ 19%] Linking CXX executable ../../bin/test_modifier +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_modifier.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_modifier.dir/test_modifier.cpp.o -o ../../bin/test_modifier -lrt -lz -lbz2 +[ 19%] Built target test_parse_lm +make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/depend.internal". +Scanning dependencies of target test_score +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/score/CMakeFiles/test_score.dir/test_score.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_score.dir/test_score.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/score/test_score.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_modifier +make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/depend.internal". +Scanning dependencies of target test_seeds_combination +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/seeds/CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp +[ 19%] Linking CXX executable ../../bin/test_random cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_random.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_random.dir/test_random.cpp.o -o ../../bin/test_random -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_random +make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/depend.internal". +Scanning dependencies of target test_seeds_extension +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Building CXX object tests/seeds/CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp:37: @@ -55620,6 +55624,47 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::ModifiedString, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::ModView, seqan::SimpleType > > > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -55746,7 +55791,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>]': @@ -55781,28 +55825,52 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::ModifiedString, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 20%] Built target test_random -make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/depend.internal". -Scanning dependencies of target test_rna_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object tests/rna_io/CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp -[ 20%] Linking CXX executable ../../bin/test_parse_lm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parse_lm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_parse_lm.dir/test_parse_lm.cpp.o -o ../../bin/test_parse_lm -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Built target test_parse_lm -make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_vstree.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ +[ 20%] Building CXX object tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::CompressedSA, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>, seqan::InfixSegment>]': @@ -55820,12 +55888,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::Owner > >, void, ReducedFMIndexConfig_>]' 143 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target test_roi_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object tests/roi_io/CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::ModView, seqan::SimpleType > > > > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -55851,47 +55944,316 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>; TIterator = seqan::ModifiedIterator*, seqan::ModView, seqan::SimpleType > > > > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::ModView, seqan::SimpleType > > > > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:95:22: required from 'void SEQAN_TEST_test_roi_roi_file_read() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:215:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = int; TCount = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:607:15: required from 'void SEQAN_TEST_test_realign_tricky_insert_window_cuts() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:666:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -55916,9 +56278,94 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple > >, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple > >, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 20%] Linking CXX executable ../../bin/test_misc -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_misc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_misc.dir/test_misc.cpp.o -o ../../bin/test_misc -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Connect_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56019,6 +56466,89 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple > >, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple > >, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:64: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = unsigned int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:395:33: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56044,6 +56574,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:41: +In member function 'seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >; unsigned int m = 3; TPack = seqan::Tag]', + inlined from 'void comparePipeStream(TPipe&, const TStrings&) [with TPipe = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Sampler<3> >; TStrings = seqan::StringSet > >]' at /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:330:9: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:203:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 203 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'void comparePipeStream(TPipe&, const TStrings&) [with TPipe = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Sampler<3> >; TStrings = seqan::StringSet > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 3 to object 'seqan::Tuple, 3, seqan::Tag >::i' with size 3 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56096,6 +56641,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple > >, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple > >, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:36: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_fm.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56200,7 +56760,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56227,12 +56786,86 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 20%] Built target test_misc -make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:280:33: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56285,10 +56918,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target test_score -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:606:11: required from 'void SEQAN_TEST_test_realign_tricky_insert_window_cuts() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:666:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56315,8 +56966,61 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 20%] Building CXX object tests/score/CMakeFiles/test_score.dir/test_score.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_score.dir/test_score.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/score/test_score.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:162:56: required from 'typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:183:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:950:54: required from 'void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:965:10: required from 'TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:363:40: required from 'void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1067:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56369,6 +57073,62 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple > >, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple > >, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56421,6 +57181,63 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Stockholm_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:162:17: required from 'typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:183:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:950:54: required from 'void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:965:10: required from 'TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:363:40: required from 'void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1067:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56473,6 +57290,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::DotBracket_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid/test_reduced_aminoacid.h:46, @@ -56526,529 +57368,55 @@ 82 | inline Triple(Triple const &_p) | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vienna_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Ebpseq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = int; TCount = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:607:15: required from 'void SEQAN_TEST_test_realign_tricky_insert_window_cuts() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:666:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:78:23: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:64: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = unsigned int; TTag = seqan::Standard_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:395:33: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -[ 20%] Linking CXX executable ../../bin/test_modifier -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_modifier.dir/link.txt --verbose=1 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:280:33: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:408:48: required from 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:47, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_modifier.dir/test_modifier.cpp.o -o ../../bin/test_modifier -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:606:11: required from 'void SEQAN_TEST_test_realign_tricky_insert_window_cuts() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:666:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:279:37: required from 'void seqan::AnsonMyersRealignmentRound_::_getReadAsProfile(seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1020:13: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:162:56: required from 'typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:183:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:950:54: required from 'void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:965:10: required from 'TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:363:40: required from 'void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1067:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:162:17: required from 'typename seqan::Source > > >::Type seqan::source(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:183:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(seqan::Iter > >&) [with TGaps = const seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:950:54: required from 'void seqan::write(TTarget&, const seqan::Gaps&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_base.h:965:10: required from 'TTarget& seqan::operator<<(TTarget&, const seqan::Gaps&) [with TTarget = std::basic_ostream; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::AnchorGaps > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:363:40: required from 'void seqan::AnsonMyersRealignmentRound_::_computeReadClippingInfo(seqan::WindowClippingInfo_&, const TAlignedReadElement&, unsigned int, unsigned int) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1067:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:81:16: required from 'void SEQAN_TEST_test_realign_one_read_no_gaps() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:653:2: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:45, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/realign/test_realign.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' @@ -57078,333 +57446,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, - from /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:41: -In member function 'seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >; unsigned int m = 3; TPack = seqan::Tag]', - inlined from 'void comparePipeStream(TPipe&, const TStrings&) [with TPipe = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Sampler<3> >; TStrings = seqan::StringSet > >]' at /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:330:9: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:203:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] - 203 | outRef->i2.i[skipped++] = 0; - | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/tests/pipe/test_pipe.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'void comparePipeStream(TPipe&, const TStrings&) [with TPipe = seqan::Pipe, seqan::Alloc<> >, seqan::Source<> >, seqan::Sampler<3> >; TStrings = seqan::StringSet > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 3 to object 'seqan::Tuple, 3, seqan::Tag >::i' with size 3 declared here - 141 | typename StoredTupleValue_::Type i[SIZE]; - | ^ -[ 20%] Linking CXX executable ../../bin/test_parallel -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_parallel.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_parallel.dir/test_parallel.cpp.o -o ../../bin/test_parallel -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:95:22: required from 'void SEQAN_TEST_test_roi_roi_file_read() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:215:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Connect_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/tests/roi_io/test_roi_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Stockholm_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::DotBracket_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vienna_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 20%] Built target test_modifier -make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Ebpseq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:55:28: required from 'void SEQAN_TEST_test_rna_io_read_connect() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:44:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Built target test_parallel -make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:40, from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: @@ -57430,18 +57471,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target test_seeds_extension -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/build -Scanning dependencies of target test_seeds_combination -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o -[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_finder.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/rna_io.h:58, from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:42, from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: @@ -57482,128 +57518,71 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:35: -/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method 'seqan::RnaRecord::RnaRecord(const seqan::RnaRecord&)' first required here - 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/rna_io.h:58, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:42, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_record.h: In instantiation of 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = seqan::RnaRecord; _Args = {seqan::RnaRecord}]': -/usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*; bool _TrivialValueTypes = false]' -/usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*]' -/usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*; _Tp = seqan::RnaRecord]' -/usr/include/c++/10/bits/stl_uninitialized.h:333:41: required from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = seqan::RnaRecord*; _ForwardIterator = seqan::RnaRecord*; _Allocator = std::allocator]' -/usr/include/c++/10/bits/vector.tcc:736:34: required from 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const seqan::RnaRecord*; _Tp = seqan::RnaRecord; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = std::vector::iterator]' -/usr/include/c++/10/bits/stl_vector.h:1665:19: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:973:11: required from 'void seqan::insert(T&&, TPosition, const TSeq&) [with T = std::vector&; TPosition = unsigned int; TSeq = seqan::RnaRecord]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_stl_container.h:910:11: required from 'typename seqan::EnableIf::Type> >, seqan::Not::Type> > >, void>::Type seqan::append(TContainer&&, const TSource&, const seqan::Tag&) [with TContainer = std::vector&; TSource = seqan::RnaRecord; TExpand = seqan::TagGenerous_; typename seqan::EnableIf::Type> >, seqan::Not::Type> > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:903:11: required from 'void seqan::append(TTarget&&, const TSource&) [with TTarget = std::vector&; TSource = seqan::RnaRecord]' -/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_struct_file.h:315:15: required from 'void seqan::readRecords(seqan::RnaStructContents&, seqan::FormattedFile, seqan::Tag, TSpec>&, TSize) [with TSpec = void; TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:355:23: required from 'void SEQAN_TEST_test_rna_io_read_ebpseq() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_record.h:119:7: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 119 | class RnaRecord - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/rna_io.h:48, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:42, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' - 104 | Align & operator=(Align const & other) - | ^~~~~~~~ -In file included from /usr/include/c++/10/bits/alloc_traits.h:33, - from /usr/include/c++/10/ext/alloc_traits.h:34, - from /usr/include/c++/10/bits/basic_string.h:40, - from /usr/include/c++/10/string:55, - from /usr/include/c++/10/bits/locale_classes.h:40, - from /usr/include/c++/10/bits/ios_base.h:41, - from /usr/include/c++/10/ios:42, - from /usr/include/c++/10/ostream:38, - from /usr/include/c++/10/iostream:39, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:35: -/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method 'seqan::RnaRecord::RnaRecord(seqan::RnaRecord&&)' first required here - 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_extension.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, +/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method 'seqan::RnaRecord::RnaRecord(const seqan::RnaRecord&)' first required here + 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/rna_io.h:58, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:42, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_record.h: In instantiation of 'void std::_Construct(_Tp*, _Args&& ...) [with _Tp = seqan::RnaRecord; _Args = {seqan::RnaRecord}]': +/usr/include/c++/10/bits/stl_uninitialized.h:91:18: required from 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*; bool _TrivialValueTypes = false]' +/usr/include/c++/10/bits/stl_uninitialized.h:150:15: required from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*]' +/usr/include/c++/10/bits/stl_uninitialized.h:325:37: required from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = seqan::RnaRecord*; _Tp = seqan::RnaRecord]' +/usr/include/c++/10/bits/stl_uninitialized.h:333:41: required from '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = seqan::RnaRecord*; _ForwardIterator = seqan::RnaRecord*; _Allocator = std::allocator]' +/usr/include/c++/10/bits/vector.tcc:736:34: required from 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const seqan::RnaRecord*; _Tp = seqan::RnaRecord; _Alloc = std::allocator; std::vector<_Tp, _Alloc>::iterator = std::vector::iterator]' +/usr/include/c++/10/bits/stl_vector.h:1665:19: [ skipping 3 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:973:11: required from 'void seqan::insert(T&&, TPosition, const TSeq&) [with T = std::vector&; TPosition = unsigned int; TSeq = seqan::RnaRecord]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/adapt_stl_container.h:910:11: required from 'typename seqan::EnableIf::Type> >, seqan::Not::Type> > >, void>::Type seqan::append(TContainer&&, const TSource&, const seqan::Tag&) [with TContainer = std::vector&; TSource = seqan::RnaRecord; TExpand = seqan::TagGenerous_; typename seqan::EnableIf::Type> >, seqan::Not::Type> > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:903:11: required from 'void seqan::append(TTarget&&, const TSource&) [with TTarget = std::vector&; TSource = seqan::RnaRecord]' +/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_struct_file.h:315:15: required from 'void seqan::readRecords(seqan::RnaStructContents&, seqan::FormattedFile, seqan::Tag, TSpec>&, TSize) [with TSpec = void; TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:355:23: required from 'void SEQAN_TEST_test_rna_io_read_ebpseq() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/rna_io/rna_record.h:119:7: warning: implicitly-declared 'seqan::Align, seqan::Alloc<> >, seqan::Tag >::Align(const seqan::Align, seqan::Alloc<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 119 | class RnaRecord + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/rna_io.h:48, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.h:42, + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' + 104 | Align & operator=(Align const & other) + | ^~~~~~~~ +In file included from /usr/include/c++/10/bits/alloc_traits.h:33, + from /usr/include/c++/10/ext/alloc_traits.h:34, + from /usr/include/c++/10/bits/basic_string.h:40, + from /usr/include/c++/10/string:55, + from /usr/include/c++/10/bits/locale_classes.h:40, + from /usr/include/c++/10/bits/ios_base.h:41, + from /usr/include/c++/10/ios:42, + from /usr/include/c++/10/ostream:38, + from /usr/include/c++/10/iostream:39, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:150, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_combination.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/tests/rna_io/test_rna_io.cpp:35: +/usr/include/c++/10/bits/stl_construct.h:109:7: note: synthesized method 'seqan::RnaRecord::RnaRecord(seqan::RnaRecord&&)' first required here + 109 | { ::new(static_cast(__p)) _Tp(std::forward<_Args>(__args)...); } + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +In member function 'seqan::Pipe >& seqan::Pipe >::operator++() [with TInput = seqan::Pipe >, seqan::Source<> >, seqan::Caster >; unsigned int m = 3; TPack = seqan::Tag]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::Source<> >, seqan::Caster >, seqan::Sampler<3> >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:203:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 203 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe >, seqan::Source<> >, seqan::Caster >, seqan::Sampler<3> >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 3 to object 'seqan::Tuple >::i' with size 3 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, @@ -57645,11 +57624,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 21%] Linking CXX executable ../../bin/test_pipe -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_pipe.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_pipe.dir/test_pipe.cpp.o -o ../../bin/test_pipe -lrt -lz -lbz2 +[ 20%] Linking CXX executable ../../bin/test_seeds_combination +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_combination.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o -o ../../bin/test_seeds_combination -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_pipe +[ 20%] Built target test_seeds_combination make -f tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_base.dir/DependInfo.cmake --color= @@ -57659,8 +57638,73 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_base.dir/test_seeds_seed_base.cpp.o +[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_base.dir/test_seeds_seed_base.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_base.dir/test_seeds_seed_base.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_base.cpp +[ 20%] Linking CXX executable ../../bin/test_pipe +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_pipe.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_pipe.dir/test_pipe.cpp.o -o ../../bin/test_pipe -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Built target test_pipe +make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend.internal". +Scanning dependencies of target test_seeds_seed_chained +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_chained.cpp +[ 20%] Linking CXX executable ../../bin/test_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_score.dir/test_score.cpp.o -o ../../bin/test_score -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Built target test_score +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend.internal". +[ 20%] Linking CXX executable ../../bin/test_seeds_extension +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_extension.dir/link.txt --verbose=1 +Scanning dependencies of target test_seeds_seed_set_unordered +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o -o ../../bin/test_seeds_extension -lrt -lz -lbz2 +[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_unordered.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Built target test_seeds_extension +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:44, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ +Scanning dependencies of target test_seeds_seed_set_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -57714,43 +57758,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 21%] Linking CXX executable ../../bin/test_seeds_combination -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_combination.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_combination.dir/test_seeds_combination.cpp.o -o ../../bin/test_seeds_combination -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_seeds_combination -make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend.internal". -Scanning dependencies of target test_seeds_seed_chained -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_chained.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_base.cpp:38: @@ -57788,9 +57795,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 21%] Linking CXX executable ../../bin/test_seeds_extension -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_extension.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_extension.dir/test_seeds_extension.cpp.o -o ../../bin/test_seeds_extension -lrt -lz -lbz2 +[ 20%] Linking CXX executable ../../bin/test_index_vstree +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_vstree.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_vstree.dir/test_index_vstree.cpp.o -o ../../bin/test_index_vstree -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units/test_multiple_translation_units_2.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 20%] Linking CXX executable ../../bin/test_roi_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_roi_io.dir/link.txt --verbose=1 +[ 20%] Built target test_index_vstree +make -f tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build.make tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o -o ../../bin/test_roi_io -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_chained.cpp:37: @@ -57828,80 +57864,45 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Linking CXX executable ../../bin/test_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_score.dir/link.txt --verbose=1 -[ 21%] Built target test_seeds_extension -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_score.dir/test_score.cpp.o -o ../../bin/test_score -lrt -lz -lbz2 -Scanning dependencies of target test_seeds_seed_set_unordered -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_unordered.cpp -[ 21%] Linking CXX executable ../../bin/test_seeds_seed_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_base.dir/test_seeds_seed_base.cpp.o -o ../../bin/test_seeds_seed_base -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_score -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target test_seeds_seed_set_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_seeds_seed_base -make -f tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build.make tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/DependInfo.cmake --color= -[ 21%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/depend.internal". Scanning dependencies of target test_seeds_banded_chain_alignment_interface make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build.make tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 22%] Building CXX object tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/test_banded_chain_alignment_interface.cpp.o +[ 21%] Building CXX object tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/test_banded_chain_alignment_interface.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/test_banded_chain_alignment_interface.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp -[ 22%] Linking CXX executable ../../bin/test_roi_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_roi_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_roi_io.dir/test_roi_io.cpp.o -o ../../bin/test_roi_io -lrt -lz -lbz2 -[ 22%] Linking CXX executable ../../bin/test_seeds_seed_chained -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_chained.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o -o ../../bin/test_seeds_seed_chained -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 22%] Built target test_seeds_seed_chained +[ 21%] Built target test_roi_io make -f tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 22%] Built target test_roi_io -make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend -[ 22%] Linking CXX executable ../../bin/test_multiple_translation_units -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_multiple_translation_units.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o -o ../../bin/test_multiple_translation_units -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend.internal". Scanning dependencies of target test_seeds_seed_diagonal make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/test_seeds_seed_diagonal.cpp.o +[ 22%] Building CXX object tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/test_seeds_seed_diagonal.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_seed_diagonal.dir/test_seeds_seed_diagonal.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_diagonal.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:43: +In member function 'seqan::Pipe, TPair, TLimitsString> >& seqan::Pipe, TPair, TLimitsString> >::operator++() [with TInput = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >; unsigned int m = 7; TPack = seqan::Tag; TPair = seqan::Pair >; TLimitsString = seqan::String >]', + inlined from 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]' at /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1330:13: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_sampler.h:470:49: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] + 470 | outRef->i2.i[skipped++] = 0; + | ~~~~~~~~~~~~~~~~~~~~~~~~^~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_creation.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h: In function 'bool seqan::append(seqan::Pool&, TSource&) [with TValue = seqan::Pair >, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple >, seqan::Tag >, int>, unsigned int, seqan::File > > >; TSource = seqan::Pipe > > >, seqan::Source<> >, seqan::Caster >, seqan::Multi >, seqan::Pair >, seqan::String > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/tuple_base.h:141:46: note: at offset 7 to object 'seqan::Tuple >::i' with size 7 declared here + 141 | typename StoredTupleValue_::Type i[SIZE]; + | ^ +[ 22%] Linking CXX executable ../../bin/test_seeds_seed_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_base.dir/test_seeds_seed_base.cpp.o -o ../../bin/test_seeds_seed_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_unordered.cpp:37: @@ -57939,15 +57940,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Built target test_seeds_seed_base +make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend.internal". Scanning dependencies of target test_seeds_global_chaining make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Building CXX object tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/test_seeds_global_chaining.cpp.o +[ 22%] Building CXX object tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/test_seeds_global_chaining.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_global_chaining.dir/test_seeds_global_chaining.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_global_chaining.cpp +[ 22%] Linking CXX executable ../../bin/test_seeds_seed_chained +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_chained.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_chained.dir/test_seeds_seed_chained.cpp.o -o ../../bin/test_seeds_seed_chained -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); @@ -57957,13 +57968,13 @@ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:43: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); | ^~~~~~ @@ -57972,7 +57983,7 @@ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:43: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ @@ -57982,9 +57993,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Built target test_seeds_seed_chained +make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend.internal". +Scanning dependencies of target test_seeds_align_banded_chain_impl +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Building CXX object tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp +[ 22%] Linking CXX executable ../../bin/test_seeds_seed_set_unordered +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_set_unordered.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o -o ../../bin/test_seeds_seed_set_unordered -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Built target test_seeds_seed_set_unordered +make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/depend.internal". +Scanning dependencies of target test_seq_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Building CXX object tests/seq_io/CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); @@ -57994,13 +58034,13 @@ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); | ^~~~~~ @@ -58009,7 +58049,7 @@ | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_set_base.cpp:40: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ @@ -58019,85 +58059,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Built target test_multiple_translation_units -make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend.internal". -Scanning dependencies of target test_seeds_align_banded_chain_impl -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Building CXX object tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp -[ 23%] Linking CXX executable ../../bin/test_seeds_seed_set_unordered -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_set_unordered.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_set_unordered.dir/test_seeds_seed_set_unordered.cpp.o -o ../../bin/test_seeds_seed_set_unordered -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Built target test_seeds_seed_set_unordered -make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Scanning dependencies of target test_seq_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Building CXX object tests/seq_io/CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_seed_diagonal.cpp:37: @@ -58135,25 +58096,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ +[ 22%] Linking CXX executable ../../bin/test_index_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_finder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_finder.dir/test_index_finder.cpp.o -o ../../bin/test_index_finder -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 22%] Built target test_index_finder +make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/depend +[ 22%] Linking CXX executable ../../bin/test_multiple_translation_units +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_multiple_translation_units.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units.cpp.o CMakeFiles/test_multiple_translation_units.dir/test_multiple_translation_units_2.cpp.o -o ../../bin/test_multiple_translation_units -lrt -lz -lbz2 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/depend.internal". +Scanning dependencies of target test_stringset_v2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 23%] Building CXX object tests/sequence/CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 23%] Built target test_multiple_translation_units +make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/depend.internal". +Scanning dependencies of target test_sequence_v2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 24%] Building CXX object tests/sequence/CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp +[ 24%] Linking CXX executable ../../bin/test_seeds_seed_diagonal +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_diagonal.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_seeds_global_chaining.cpp:37: @@ -58191,34 +58167,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:419:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::String, TStringSpec>&, const seqan::StringSet&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSize = unsigned int; TFragmentSpec = seqan::ExactFragment<>; TStringSpec = seqan::Alloc<>; TSequence = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:1950:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_fragments_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2526:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_diagonal.dir/test_seeds_seed_diagonal.cpp.o -o ../../bin/test_seeds_seed_diagonal -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 24%] Built target test_seeds_seed_diagonal +make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/depend.internal". +Scanning dependencies of target test_sequence +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 24%] Building CXX object tests/sequence/CMakeFiles/test_sequence.dir/test_sequence.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence.dir/test_sequence.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: @@ -58256,88 +58218,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' @@ -58345,9 +58230,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -58358,16 +58243,8 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' @@ -58375,111 +58252,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 23%] Linking CXX executable ../../bin/test_seeds_seed_diagonal -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_diagonal.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_diagonal.dir/test_seeds_seed_diagonal.cpp.o -o ../../bin/test_seeds_seed_diagonal -lrt -lz -lbz2 -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' @@ -58487,9 +58277,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -58500,457 +58290,29 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Built target test_seeds_seed_diagonal -make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/depend.internal". -Scanning dependencies of target test_stringset_v2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 24%] Building CXX object tests/sequence/CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:419:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::String, TStringSpec>&, const seqan::StringSet&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSize = unsigned int; TFragmentSpec = seqan::ExactFragment<>; TStringSpec = seqan::Alloc<>; TSequence = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:1950:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_fragments_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2526:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] 647 | return Iter >(container(left), hostIterator(left) - right); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 586 | return Iter >(container(left), hostIterator(left) + right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, @@ -59001,525 +58363,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/seq_io/test_write_bam.h:51:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -[ 24%] Linking CXX executable ../../bin/test_seeds_global_chaining -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_global_chaining.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_global_chaining.dir/test_seeds_global_chaining.cpp.o -o ../../bin/test_seeds_global_chaining -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:419:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::String, TStringSpec>&, const seqan::StringSet&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSize = unsigned int; TFragmentSpec = seqan::ExactFragment<>; TStringSpec = seqan::Alloc<>; TSequence = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:1950:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_fragments_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2526:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -[ 24%] Built target test_seeds_global_chaining -make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/depend.internal". -Scanning dependencies of target test_sequence_v2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/sequence/CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: @@ -59601,6 +58444,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: @@ -59682,33 +58550,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: @@ -59790,16 +58656,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_seeds_seed_set_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_set_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o -o ../../bin/test_seeds_seed_set_base -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' @@ -59809,9 +58689,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -59819,241 +58699,221 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_seeds_seed_set_base -make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/depend -[ 25%] Linking CXX executable ../../bin/test_realign -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_realign.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_realign.dir/test_realign.cpp.o -o ../../bin/test_realign -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/depend.internal". -Scanning dependencies of target test_sequence -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) | ^~~~~~~~ -[ 25%] Building CXX object tests/sequence/CMakeFiles/test_sequence.dir/test_sequence.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence.dir/test_sequence.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = seqan::String, seqan::Packed<> >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = seqan::String, seqan::Packed<> >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -[ 25%] Built target test_realign -make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend.internal". -Scanning dependencies of target test_sequence_journaled -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = char (&)[5]]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = char (&)[5]]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -[ 25%] Building CXX object tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = seqan::String, seqan::Packed<> >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = seqan::String, seqan::Packed<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = char (&)[5]]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = const seqan::String, seqan::Packed<> >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = const seqan::String, seqan::Packed<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = seqan::String, seqan::Packed<> >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = seqan::String, seqan::Packed<> >&]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, - from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/seq_io/test_write_bam.h:51:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:42: /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h: In instantiation of 'void SEQAN_TEST_Combinatoric() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:91:2: required from here @@ -60170,6 +59030,111 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/seq_io/test_read_bam.h:53:51: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seq_io/test_seq_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::__cxx11::list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::__cxx11::list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1769 | ref = 'G'; + | ~~~~^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::__cxx11::list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::__cxx11::list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1371 | val = 'A'; + | ~~~~^~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::__cxx11::list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::__cxx11::list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1062 | val = 'A'; + | ~~~~^~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:42: /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h: In instantiation of 'void Test_Assignments_Combinatoric(TTarget&, TSource, seqan::Tag, size_t) [with TTarget = seqan::String >; TSource = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagExact_; size_t = unsigned int]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:1191:34: required from 'void SEQAN_TEST_Combinatoric() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' @@ -60194,6 +59159,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_crosscompare_dna.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String, seqan::Packed<> >; TSpec = seqan::Owner >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:42: /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h: In instantiation of 'void Test_Assignments_Combinatoric(TTarget&, TSource, seqan::Tag, size_t) [with TTarget = seqan::String >; TSource = seqan::Segment >, seqan::InfixSegment>; TExpand = seqan::TagLimit_; size_t = unsigned int]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:1193:34: required from 'void SEQAN_TEST_Combinatoric() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' @@ -60206,17 +59178,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::__cxx11::list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::__cxx11::list]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1769 | ref = 'G'; - | ~~~~^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ +[ 24%] Linking CXX executable ../../bin/test_seeds_global_chaining +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_global_chaining.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_global_chaining.dir/test_seeds_global_chaining.cpp.o -o ../../bin/test_seeds_global_chaining -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:36: @@ -60237,8 +59201,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::__cxx11::list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::__cxx11::list]' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::forward_list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::forward_list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1769 | ref = 'G'; + | ~~~~^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ +[ 24%] Built target test_seeds_global_chaining +make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/DependInfo.cmake --color= +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::forward_list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::forward_list]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1371 | val = 'A'; @@ -60246,8 +59226,8 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::__cxx11::list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::__cxx11::list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::forward_list]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::forward_list]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1062 | val = 'A'; @@ -60255,6 +59235,8 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend.internal". /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = char*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:64: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_string.h:815:5: required from 'void SEQAN_TEST_Segment() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' @@ -60282,12 +59264,264 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_index_creation -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_creation.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o -o ../../bin/test_index_creation -lrt -lz -lbz2 +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +Scanning dependencies of target test_sequence_journaled +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 24%] Building CXX object tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::forward_list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::forward_list]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::deque]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::deque]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1769 | ref = 'G'; @@ -60296,6 +59530,15 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::deque]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::deque]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1371 | val = 'A'; + | ~~~~^~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': @@ -60443,6 +59686,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::deque]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::deque]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] + 1062 | val = 'A'; + | ~~~~^~~~~ +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' + 69 | CountingChar(CountingChar const & other) : value(other.value) + | ^~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': @@ -60464,24 +59716,59 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::forward_list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::forward_list]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1371 | val = 'A'; - | ~~~~^~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::forward_list]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::forward_list]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1062 | val = 'A'; - | ~~~~^~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': @@ -60497,6 +59784,101 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_index_fm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_fm.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::SuffixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_fm.dir/test_index_fm.cpp.o -o ../../bin/test_index_fm -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': @@ -60515,8 +59897,8 @@ 129 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::deque]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::deque]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::vector]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::vector]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1769 | ref = 'G'; @@ -60525,8 +59907,8 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::deque]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::deque]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::vector]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::vector]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1371 | val = 'A'; @@ -60534,8 +59916,8 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::deque]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::deque]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::vector]': +/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::vector]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] 1062 | val = 'A'; @@ -60543,6 +59925,9 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_seeds_seed_set_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_seed_set_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_seed_set_base.dir/test_seeds_seed_set_base.cpp.o -o ../../bin/test_seeds_seed_set_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:36: @@ -60562,6 +59947,83 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = char]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_seeds_seed_set_base +make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/depend.internal". +Scanning dependencies of target test_simd_vector +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object tests/simd/CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.cpp +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:419:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::String, TStringSpec>&, const seqan::StringSet&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSize = unsigned int; TFragmentSpec = seqan::ExactFragment<>; TStringSpec = seqan::Alloc<>; TSequence = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:1950:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_fragments_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2526:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 586 | return Iter >(container(left), hostIterator(left) + right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment; typename seqan::Iterator >::Type = seqan::Iter, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': @@ -60588,6 +60050,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment; TIterator = char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = seqan::String, seqan::Packed<> >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = seqan::String, seqan::Packed<> >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = char; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -60610,122 +60091,330 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = char]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = std::vector]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = std::vector]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1805:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1769:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1769 | ref = 'G'; - | ~~~~^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = std::vector]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = std::vector]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1371:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1371 | val = 'A'; - | ~~~~^~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceBack(TString&) [with TString = std::vector]': -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1084:21: required from 'void StringTestCommon__Back::runTest() [with SEQAN_TParam = std::vector]' -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1079:1: required from here -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1062:9: warning: implicitly-declared 'constexpr CountingChar& CountingChar::operator=(const CountingChar&)' is deprecated [-Wdeprecated-copy] - 1062 | val = 'A'; - | ~~~~^~~~~ -/build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' - 69 | CountingChar(CountingChar const & other) : value(other.value) - | ^~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_helpers.h:42, + from /build/seqan2-2.4.0+dfsg/tests/index/test_index_base.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String, seqan::Alloc<> >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 25%] Built target test_index_fm +make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend.internal". +Scanning dependencies of target test_simple_intervals_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = char (&)[5]]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = char (&)[5]]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = seqan::String, seqan::Packed<> >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = seqan::String, seqan::Packed<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const char (&)[5]; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const char (&)[5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = char [5]; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = char (&)[5]]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2259:16: required from 'void StringSetTestCommon__SuffixOnValue::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:2249:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +[ 25%] Building CXX object tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/simple_intervals_io/test_simple_intervals_io.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = char; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String >*; TParam = const seqan::String >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = const seqan::String >&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String >; TString2 = seqan::String >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet >, seqan::Owner<> >&; TSource = seqan::String >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = short int; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = const seqan::String, seqan::Packed<> >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::String, seqan::Packed<> >*; TParam = const seqan::String, seqan::Packed<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Packed<> >, seqan::Alloc<> >; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::String, seqan::Packed<> >; TTargetSpec = seqan::Alloc<>; TValue = const seqan::String, seqan::Packed<> >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::String, seqan::Packed<> >; TString2 = seqan::String, seqan::Packed<> >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >&; TSource = seqan::String, seqan::Packed<> >&]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1826:16: required from 'void testStringSetValue(TStringSet&) [with TStringSet = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1898:23: required from 'void StringSetTestCommon__Value::runTest() [with SEQAN_TParam = seqan::StringSet, seqan::Packed<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:1893:1: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'seqan::String, seqan::Packed<> >::String(const seqan::String, seqan::Packed<> >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_string_set.h:43, + from /build/seqan2-2.4.0+dfsg/tests/sequence/test_stringset_v2.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String, seqan::Packed<> >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = seqan::SimpleType; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 351 | return TIterator(me, begin(me, Standard())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:37: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_index_creation -make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/depend.internal". -Scanning dependencies of target test_simd_vector -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/simd/CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/simd/test_simd_vector.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = seqan::String >]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = seqan::String >]' @@ -60755,6 +60444,72 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In function 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Packed<> >; TAlgSpec = seqan::Skew7]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:102:9: warning: '' is used uninitialized in this function [-Wuninitialized] + 102 | data_iterator = TIterator(); + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = seqan::String >]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = seqan::String >]' @@ -60784,6 +60539,31 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::SuffixSegment>; TSequenceV = seqan::Segment >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:40: /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceValue(TString&) [with TString = seqan::String >]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1810:22: required from 'void StringTestCommon__Value::runTest() [with SEQAN_TParam = seqan::String >]' @@ -60813,6 +60593,133 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String >, seqan::Alloc<> >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:245:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, unsigned int) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; TSeeds = seqan::String >, seqan::Alloc<> >; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1012:35: required from 'void SEQAN_TEST_test_banded_chain_alignment_issue_1020() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1109:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::SeedSet >, seqan::Tag >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:221:32: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::SeedSet >, seqan::Tag >; TScoreValue = int; TScoreSpec = seqan::Tag; bool TFirstRow = true; bool TFirstColumn = true; bool TLastColumn = true; bool TLastRow = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:68:37: required from 'void testBandedChainAlignmentEmptyChain(const TGapCosts&) [with TGapCosts = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1020:39: required from 'void SEQAN_TEST_test_banded_chain_alignment_empty_set_linear() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:1097:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_align_banded_chain_impl.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::__cxx11::basic_stringstream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::__cxx11::basic_stringstream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:70:14: required from 'void testJournaledStringAssign(const TStringJournalSpec&) [with TStringJournalSpec = seqan::SortedArray]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.h:1179:30: required from 'void SEQAN_TEST_test_sequence_journaled_sorted_array_assign() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/sequence_journaled/test_sequence_journaled.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = seqan::String >]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = seqan::String >]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here @@ -60831,6 +60738,71 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:41: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:510:37: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_simd_vector +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simd_vector.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o -o ../../bin/test_simd_vector -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h: In instantiation of 'void testSequenceFront(TString&) [with TString = seqan::String >]': /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1393:22: required from 'void StringTestCommon__Front::runTest() [with SEQAN_TParam = seqan::String >]' /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:1388:1: required from here @@ -60849,6 +60821,19 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_simd_vector +make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/depend.internal". +Scanning dependencies of target test_statistics +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object tests/statistics/CMakeFiles/test_statistics.dir/test_statistics.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_statistics.dir/test_statistics.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/statistics/test_statistics.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence_v2.cpp:37: @@ -60878,6 +60863,9 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_realign +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_realign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_realign.dir/test_realign.cpp.o -o ../../bin/test_realign -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:43, @@ -60990,6 +60978,31 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1336:38: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String, seqan::Alloc<> >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:419:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::String, TStringSpec>&, const seqan::StringSet&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSize = unsigned int; TFragmentSpec = seqan::ExactFragment<>; TStringSpec = seqan::Alloc<>; TSequence = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:1950:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_fragments_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2526:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:92, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:43, @@ -61070,43 +61083,8 @@ /build/seqan2-2.4.0+dfsg/tests/sequence/test_sequence.h:69:5: note: because 'CountingChar' has user-provided 'CountingChar::CountingChar(const CountingChar&)' 69 | CountingChar(CountingChar const & other) : value(other.value) | ^~~~~~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_simd_vector -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simd_vector.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_simd_vector.dir/test_simd_vector.cpp.o -o ../../bin/test_simd_vector -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_simd_vector -make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend.internal". -Scanning dependencies of target test_simple_intervals_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/simple_intervals_io/test_simple_intervals_io.cpp -[ 25%] Linking CXX executable ../../bin/test_rna_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_rna_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o -o ../../bin/test_rna_io -lrt -lz -lbz2 -[ 25%] Linking CXX executable ../../bin/test_reduced_aminoacid -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_reduced_aminoacid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o -o ../../bin/test_reduced_aminoacid -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_rna_io -make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/depend.internal". -Scanning dependencies of target test_statistics -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/statistics/CMakeFiles/test_statistics.dir/test_statistics.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_statistics.dir/test_statistics.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/statistics/test_statistics.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_reduced_aminoacid +[ 25%] Built target test_realign make -f tests/store/CMakeFiles/test_store.dir/build.make tests/store/CMakeFiles/test_store.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store/CMakeFiles/test_store.dir/DependInfo.cmake --color= @@ -61118,6 +61096,74 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object tests/store/CMakeFiles/test_store.dir/test_store.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_store.dir/test_store.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/store/test_store.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:526:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:873:34: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:201:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Align&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequence = seqan::String >; TAlignSpec = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:123:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_align_linear_global_two_scores() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2487:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_align.dir/test_align.cpp.o -o ../../bin/test_align -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:624:58: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_<>; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1264:29: required from 'typename seqan::Value::Type seqan::_computeAlignment(TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TGapScheme = seqan::Tag; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_<>; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:930:38: required from 'typename seqan::Value::Type seqan::_initializeBandedChain(TTraceSet&, TScoutState&, const TSeed&, unsigned int, const TSeqH&, const TSeqV&, const TScoreScheme&, const TScoreScheme&, const seqan::DPProfile_, TGapCosts, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSeed = seqan::Seed >; TSeqH = seqan::String >; TSeqV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGaps = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_impl.h:1319:47: required from 'TScoreValue seqan::_computeAlignment(TTraceSet&, const TSeedSet&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, unsigned int, const seqan::DPProfile_, TGapSpec, seqan::TracebackOn, TExecPolicy>&) [with TTraceSet = seqan::StringSet >, seqan::Owner<> >; TSeedSet = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; TFreeEndGaps = seqan::FreeEndGaps_<>; TDPMatrixLocation = seqan::Tag; TGapSpec = seqan::Tag; TTracebackConfig = seqan::TracebackConfig_, seqan::Tag >; TExecPolicy = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment_profile.h:258:33: required from 'TScoreValue seqan::_setupAndRunBandedChainAlignment(seqan::StringSet, TStringSetSpec>&, const TSeeds&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int, const TGapsPlacement&) [with TTraceSegment = seqan::TraceSegment_; TStringSetSpec = seqan::Owner<>; TSeeds = seqan::String > >; TSequenceH = seqan::String >; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag; TGapsPlacement = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/seeds/banded_chain_alignment.h:270:41: required from 'TScoreValue seqan::bandedChainAlignment(seqan::Gaps&, seqan::Gaps&, const TSeeds&, const seqan::Score&, const seqan::Score&, const seqan::AlignConfig&, unsigned int) [with TSequenceH = seqan::String >; TGapSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapSpecV = seqan::Tag; TSeeds = seqan::String > >; TScoreValue = int; TScoreSpecAnchor = seqan::Tag; TScoreSpecGap = seqan::Tag; bool TFirstRow = false; bool TFirstColumn = false; bool TLastColumn = false; bool TLastRow = false; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:668:42: required from 'void SEQAN_TEST_test_banded_chain_alignment_gaps_linear_global_two_score() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:2500:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/tests/seeds/test_banded_chain_alignment_interface.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_align +make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/depend.internal". +Scanning dependencies of target test_stream +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object tests/stream/CMakeFiles/test_stream.dir/test_stream.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_stream.dir/test_stream.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/statistics/test_statistics.cpp:37: @@ -61324,6 +61370,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_simple_intervals_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simple_intervals_io.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o -o ../../bin/test_simple_intervals_io -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -61474,6 +61523,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_simple_intervals_io +make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/depend +[ 25%] Linking CXX executable ../../bin/test_rna_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_rna_io.dir/link.txt --verbose=1 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:38, @@ -61496,6 +61552,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_rna_io.dir/test_rna_io.cpp.o -o ../../bin/test_rna_io -lrt -lz -lbz2 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:38, @@ -61549,6 +61608,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target test_find_swift +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -61581,6 +61644,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 25%] Building CXX object tests/swift_local/CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -61689,6 +61754,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_rna_io +make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend.internal". +Scanning dependencies of target test_tabix_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, @@ -61720,6 +61796,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 25%] Building CXX object tests/tabix_io/CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -61862,7 +61940,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_sequence_journaled /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' @@ -61905,8 +61982,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence_journaled.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o -o ../../bin/test_sequence_journaled -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:38, @@ -62052,7 +62127,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -62088,8 +62162,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 25%] Built target test_sequence_journaled -make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:38, @@ -62118,10 +62190,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/tests/store/test_store_io.h:38, @@ -62148,10 +62216,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target test_stream -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/store/test_store.cpp:37: @@ -62202,8 +62266,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 25%] Building CXX object tests/stream/CMakeFiles/test_stream.dir/test_stream.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_stream.dir/test_stream.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/stream/test_stream.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/store/test_store.cpp:37: @@ -62269,22 +62331,81 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_simple_intervals_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_simple_intervals_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_simple_intervals_io.dir/test_simple_intervals_io.cpp.o -o ../../bin/test_simple_intervals_io -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../../bin/test_reduced_aminoacid +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_reduced_aminoacid.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_reduced_aminoacid.dir/test_reduced_aminoacid.cpp.o -o ../../bin/test_reduced_aminoacid -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:42, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:51:22: required from 'void SEQAN_TEST_test_tabix_io_read_indexed_vcf() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:43:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_simple_intervals_io -make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/depend +[ 25%] Built target test_reduced_aminoacid +make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/depend.internal". -Scanning dependencies of target test_find_swift +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/depend.internal". +Scanning dependencies of target test_translation make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/build +make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/build +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:51:22: required from 'void SEQAN_TEST_test_tabix_io_read_indexed_vcf() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:43:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/swift_local/CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp +[ 25%] Building CXX object tests/translation/CMakeFiles/test_translation.dir/test_translation.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_translation.dir/test_translation.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp +[ 25%] Linking CXX executable ../../bin/test_sequence_journaled +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence_journaled.dir/link.txt --verbose=1 +[ 25%] Linking CXX executable ../../bin/test_index_creation +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence_journaled.dir/test_sequence_journaled.cpp.o -o ../../bin/test_sequence_journaled -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_creation.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_creation.dir/test_index_creation.cpp.o -o ../../bin/test_index_creation -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../../bin/test_index_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_base.dir/test_index_base.cpp.o -o ../../bin/test_index_base -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_sequence_journaled +make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, from /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:36: @@ -62320,16 +62441,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_statistics -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_statistics.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_statistics.dir/test_statistics.cpp.o -o ../../bin/test_statistics -lrt -lz -lbz2 +Scanning dependencies of target test_ucsc_io make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_statistics -make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend +make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend.internal". +[ 25%] Building CXX object tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_index_creation +make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend.internal". +Scanning dependencies of target test_vcf_io +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object tests/vcf_io/CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_index_base +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/unassigned_or_unused/tutorials_custim_io/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/unassigned_or_unused/tutorials_custim_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution3.cpp /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp: In instantiation of 'seqan::Align > testLongestEpsMatch(const TString&, const TString&) [with TString = seqan::String, seqan::Alloc<> >]': /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:219:53: required from 'void SEQAN_TEST_test_longest_epsMatch() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:321:5: required from here @@ -62342,10 +62485,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> > >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -Scanning dependencies of target test_tabix_io -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Linking CXX executable ../../bin/test_index_crosscompare_dna +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_crosscompare_dna.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_crosscompare_dna.dir/test_index_crosscompare_dna.cpp.o -o ../../bin/test_index_crosscompare_dna -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:40: /build/seqan2-2.4.0+dfsg/tests/swift_local/../../apps/stellar/stellar.h: In instantiation of 'void _splitAtXDrops(TAlign&, seqan::Score >&, TScoreValue1, TScoreValue2, seqan::String&) [with TAlign = seqan::Align, seqan::Alloc<> > >; TScoreValue = int; TScoreValue1 = int; TScoreValue2 = int]': /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:246:19: required from 'void testXDropAlign(const TString&, const TString&, TScore, TScoreValue, TScoreValue, TAliString&) [with TString = seqan::String, seqan::Alloc<> >; TScore = seqan::Score >; TAliString = seqan::String, seqan::Alloc<> > > >; TScoreValue = int]' @@ -62360,8 +62502,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> > >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -[ 25%] Building CXX object tests/tabix_io/CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp +[ 25%] Linking CXX executable ../../bin/test_index_bifm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_index_bifm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_index_bifm.dir/test_index_bifm.cpp.o -o ../../bin/test_index_bifm -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:37: @@ -62421,6 +62564,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index, seqan::Alloc<> > >, seqan::IndexQGram > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::StringSet, seqan::Alloc<> > >; TShapeSpec = seqan::UngappedShape<4>; TSpec = seqan::Tag]' 278 | Index(Index const &other): | ^~~~~ +[ 25%] Linking CXX executable ../../bin/test_statistics +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_statistics.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_statistics.dir/test_statistics.cpp.o -o ../../bin/test_statistics -lrt -lz -lbz2 +[ 25%] Built target test_index_crosscompare_dna +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/tests/swift_local/test_find_swift.cpp:36: @@ -62463,97 +62614,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> > >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:42, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:51:22: required from 'void SEQAN_TEST_test_tabix_io_read_indexed_vcf() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:43:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.h:51:22: required from 'void SEQAN_TEST_test_tabix_io_read_indexed_vcf() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:43:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/tabix_io/test_tabix_io.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_seq_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seq_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o -o ../../bin/test_seq_io -lrt -lz -lbz2 -[ 25%] Linking CXX executable ../../bin/test_tabix_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tabix_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o -o ../../bin/test_tabix_io -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_tabix_io -make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/depend.internal". -[ 25%] Built target test_seq_io -make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend +[ 25%] Built target test_statistics +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend.internal". -Scanning dependencies of target test_translation +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/translation/CMakeFiles/test_translation.dir/test_translation.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_translation.dir/test_translation.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp -Scanning dependencies of target test_ucsc_io +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution2.cpp +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp -[ 25%] Linking CXX executable ../../bin/test_find_swift -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find_swift.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o -o ../../bin/test_find_swift -lrt -lz -lbz2 +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution1.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_find_swift -make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend +[ 25%] Built target test_index_bifm +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend.internal". -Scanning dependencies of target test_vcf_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object tests/vcf_io/CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_ENABLE_TESTING=1 -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o -c /build/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.cpp +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:40: @@ -62616,6 +62710,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::SuffixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:499:13: required from 'void test_translation_stringset_multiframe_impl(const TResultSet&, const TSourceSet&, const TParallelism&) [with TSourceSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TResultSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TParallelism = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:583:51: required from 'void test_translation_stringset_multiframe_impl0() [with TSetSpec = seqan::Owner >; TParallelism = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:650:79: required from 'void SEQAN_TEST_test_translation_stringset_multiframe_concatdirect_serial() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:49:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Ucsc_]': @@ -62640,6 +62755,34 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:290:37: required from 'void seqan::_translateImplLoop(seqan::StringSet, TSpec1>, TSpec2>&, unsigned int, const seqan::StringSet&, const seqan::GeneticCode&, const seqan::Frames_<6>&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TSpec3 = seqan::Dependent >; TInString = seqan::String, seqan::Alloc<> >; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL]' +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:331:31: required from 'void seqan::_translateImplLoopOMPWrapper(TTarget&, const TSource&, const seqan::GeneticCode&, const seqan::Frames_&, const Serial&) [with TSource = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TTarget = seqan::StringSet, seqan::Alloc<> > >; unsigned char frames = 6; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; seqan::Serial = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:361:33: required from 'void seqan::_translateImpl(seqan::StringSet, TSpec1>, TSpec2>&, const seqan::StringSet&, const seqan::GeneticCode&, const seqan::Frames_&, const TParallelism&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TSpec3 = seqan::Dependent >; TInString = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; unsigned char n = 6]' +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:428:19: required from 'void seqan::_translateInputWrap(seqan::StringSet, TSpec1>, TSpec2>&, const TInString&, const seqan::GeneticCode&, const seqan::Frames_&, const TParallelism&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TInString = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; unsigned char n = 6]' +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:538:35: required from 'void seqan::translate(TTarget&, const TSource&, seqan::TranslationFrames, const seqan::GeneticCode&, const TParallelism&) [with TTarget = seqan::StringSet, seqan::Alloc<> > >; TSource = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL]' +/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:589:21: required from 'void seqan::translate(TTarget&, const TSource&, seqan::TranslationFrames, const TParallelism&) [with TTarget = seqan::StringSet, seqan::Alloc<> > >; TSource = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:420:18: required from 'void test_translation_onestring_multiframe_impl() [with TTargetSet = seqan::StringSet, seqan::Alloc<> > >; TParallelism = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:460:64: required from 'void SEQAN_TEST_test_translation_onestring_multiframe_serial() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' +/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:46:5: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] + 141 | _cargo() + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/tests/ucsc_io/test_ucsc_io.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -62677,55 +62820,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:947:29: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*, const char*, ...) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:998:21: required from 'bool seqan::ClassTest::testEqual(const char*, int, const T1&, const char*, const T2&, const char*) [with T1 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; T2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:499:13: required from 'void test_translation_stringset_multiframe_impl(const TResultSet&, const TSourceSet&, const TParallelism&) [with TSourceSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TResultSet = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TParallelism = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:583:51: required from 'void test_translation_stringset_multiframe_impl0() [with TSetSpec = seqan::Owner >; TParallelism = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:650:79: required from 'void SEQAN_TEST_test_translation_stringset_multiframe_concatdirect_serial() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:49:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'seqan::ModifiedString::ModifiedString(THost_&&, typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type*) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&; THost = seqan::ModifiedString, seqan::Alloc<> >, seqan::PrefixSegment>, seqan::ModView > > >; TSpec = seqan::Tag; typename seqan::EnableIf::Type, typename seqan::RemoveReference::Type> >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:290:37: required from 'void seqan::_translateImplLoop(seqan::StringSet, TSpec1>, TSpec2>&, unsigned int, const seqan::StringSet&, const seqan::GeneticCode&, const seqan::Frames_<6>&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TSpec3 = seqan::Dependent >; TInString = seqan::String, seqan::Alloc<> >; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL]' -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:331:31: required from 'void seqan::_translateImplLoopOMPWrapper(TTarget&, const TSource&, const seqan::GeneticCode&, const seqan::Frames_&, const Serial&) [with TSource = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TTarget = seqan::StringSet, seqan::Alloc<> > >; unsigned char frames = 6; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; seqan::Serial = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:361:33: required from 'void seqan::_translateImpl(seqan::StringSet, TSpec1>, TSpec2>&, const seqan::StringSet&, const seqan::GeneticCode&, const seqan::Frames_&, const TParallelism&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TSpec3 = seqan::Dependent >; TInString = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; unsigned char n = 6]' -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:428:19: required from 'void seqan::_translateInputWrap(seqan::StringSet, TSpec1>, TSpec2>&, const TInString&, const seqan::GeneticCode&, const seqan::Frames_&, const TParallelism&) [with TSpec1 = seqan::Alloc<>; TSpec2 = seqan::Owner<>; TInString = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL; unsigned char n = 6]' -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:538:35: required from 'void seqan::translate(TTarget&, const TSource&, seqan::TranslationFrames, const seqan::GeneticCode&, const TParallelism&) [with TTarget = seqan::StringSet, seqan::Alloc<> > >; TSource = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag; seqan::GeneticCodeSpec CODE_SPEC = seqan::CANONICAL]' -/build/seqan2-2.4.0+dfsg/include/seqan/translation/translation.h:589:21: required from 'void seqan::translate(TTarget&, const TSource&, seqan::TranslationFrames, const TParallelism&) [with TTarget = seqan::StringSet, seqan::Alloc<> > >; TSource = seqan::String, seqan::Alloc<> >; TParallelism = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:420:18: required from 'void test_translation_onestring_multiframe_impl() [with TTargetSet = seqan::StringSet, seqan::Alloc<> > >; TParallelism = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.h:460:64: required from 'void SEQAN_TEST_test_translation_onestring_multiframe_serial() [with bool speed_up_dummy_to_prevent_compilation_of_unused_tests_ = true]' -/build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:46:5: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:141:20: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>&)' is deprecated [-Wdeprecated-copy] - 141 | _cargo() - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>; TFunctor = seqan::FunctorComplement >; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::PrefixSegment>]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/tests/translation/test_translation.cpp:38: @@ -63004,92 +63098,28 @@ from /build/seqan2-2.4.0+dfsg/tests/vcf_io/test_vcf_io.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 25%] Linking CXX executable ../../bin/test_sequence -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence.dir/test_sequence.cpp.o -o ../../bin/test_sequence -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_sequence -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/unassigned_or_unused/tutorials_custim_io/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/unassigned_or_unused/tutorials_custim_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution3.cpp + | ^~~~~~~~ [ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution3 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/unassigned_or_unused/tutorials_custim_io/solution3.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution3 -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution2.cpp -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution2 -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution1.cpp -[ 25%] Linking CXX executable ../../bin/test_ucsc_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_ucsc_io.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o -o ../../bin/test_ucsc_io -lrt -lz -lbz2 -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake --color= -[ 25%] Built target test_ucsc_io make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/unassigned_or_unused/tutorial_sequence/sequence_all_strings.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/unassigned_or_unused/tutorial_sequence/sequence_all_strings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/sequence_all_strings.cpp -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/unassigned_or_unused/tutorials_custim_io/solution2.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution2 make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/DependInfo.cmake --color= @@ -63101,11 +63131,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/unassigned_or_unused/tutorial_sequence/replace_as.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/unassigned_or_unused/tutorial_sequence/replace_as.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/replace_as.cpp -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/unassigned_or_unused/tutorial_sequence/sequence_all_strings.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/unassigned_or_unused/tutorials_custim_io/solution1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution1 make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/DependInfo.cmake --color= @@ -63117,40 +63147,46 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/unassigned_or_unused/tutorials_custim_io/reader_demo.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/unassigned_or_unused/tutorials_custim_io/reader_demo.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/reader_demo.cpp -[ 25%] Linking CXX executable ../../bin/test_stream -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_stream.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_stream.dir/test_stream.cpp.o -o ../../bin/test_stream -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/unassigned_or_unused/tutorial_sequence/sequence_iterator_demo.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_stream +[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/depend.internal". -[ 25%] Linking CXX executable ../../bin/test_vcf_io -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_vcf_io.dir/link.txt --verbose=1 Scanning dependencies of target demo_unassigned_or_unused_tutorial_file_io_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o -o ../../bin/test_vcf_io -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/unassigned_or_unused/tutorial_file_io/solution1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/unassigned_or_unused/tutorial_file_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/solution1.cpp +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/unassigned_or_unused/tutorial_sequence/sequence_all_strings.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings +make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_sam2svg +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp [ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_replace_as cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/unassigned_or_unused/tutorial_sequence/replace_as.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_replace_as -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_replace_as -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake --color= -[ 25%] Built target test_vcf_io make -f demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/depend.internal". Scanning dependencies of target demo_unassigned_or_unused_rooted_iterator @@ -63162,13 +63198,7 @@ [ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_reader_demo cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/unassigned_or_unused/tutorials_custim_io/reader_demo.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_reader_demo -lrt -lz -lbz2 -Scanning dependencies of target demo_unassigned_or_unused_sam2svg -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp [ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_reader_demo make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' @@ -63181,38 +63211,38 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/unassigned_or_unused/modifier_nested.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/unassigned_or_unused/modifier_nested.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/modifier_nested.cpp -[ 25%] Linking CXX executable ../../bin/test_translation -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_translation.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_translation.dir/test_translation.cpp.o -o ../../bin/test_translation -lrt -lz -lbz2 +[ 25%] Linking CXX executable ../../bin/test_tabix_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_tabix_io.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_tabix_io.dir/test_tabix_io.cpp.o -o ../../bin/test_tabix_io -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_tabix_io +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_modifier_modview +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/unassigned_or_unused/modifier_modview.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/unassigned_or_unused/modifier_modview.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/modifier_modview.cpp [ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_rooted_iterator cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/unassigned_or_unused/rooted_iterator.cpp.o -o ../bin/demo_unassigned_or_unused_rooted_iterator -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Built target demo_unassigned_or_unused_rooted_iterator -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/DependInfo.cmake --color= -[ 25%] Built target test_translation make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/depend.internal". Scanning dependencies of target demo_unassigned_or_unused_modifier_modreverse make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build -Scanning dependencies of target demo_unassigned_or_unused_modifier_modview -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/unassigned_or_unused/modifier_modreverse.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/unassigned_or_unused/modifier_modreverse.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/modifier_modreverse.cpp -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/unassigned_or_unused/modifier_modview.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/unassigned_or_unused/modifier_modview.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/modifier_modview.cpp [ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_modifier_nested cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/unassigned_or_unused/modifier_nested.cpp.o -o ../bin/demo_unassigned_or_unused_modifier_nested -lrt -lz -lbz2 @@ -63245,9 +63275,6 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/unassigned_or_unused/index_supermaxrepeats.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/unassigned_or_unused/index_supermaxrepeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_supermaxrepeats.cpp -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_modifier_modreverse -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/unassigned_or_unused/modifier_modreverse.cpp.o -o ../bin/demo_unassigned_or_unused_modifier_modreverse -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp:5: @@ -63267,7 +63294,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -63295,18 +63321,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 25%] Built target demo_unassigned_or_unused_modifier_modreverse -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_index_sufarray -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_sufarray.cpp +[ 25%] Linking CXX executable ../../bin/test_ucsc_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_ucsc_io.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_ucsc_io.dir/test_ucsc_io.cpp.o -o ../../bin/test_ucsc_io -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sam2svg.cpp:5: @@ -63402,6 +63419,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/unassigned_or_unused/tutorial_file_io/solution1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_solution1 -lrt -lz -lbz2 +[ 25%] Built target test_ucsc_io +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend.internal". +[ 25%] Linking CXX executable ../../bin/test_find_swift +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_find_swift.dir/link.txt --verbose=1 +Scanning dependencies of target demo_unassigned_or_unused_index_sufarray +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_find_swift.dir/test_find_swift.cpp.o -o ../../bin/test_find_swift -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_sufarray.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -63459,6 +63495,42 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target demo_unassigned_or_unused_tutorial_file_io_solution1 +[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_modifier_modreverse +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/link.txt --verbose=1 +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/unassigned_or_unused/modifier_modreverse.cpp.o -o ../bin/demo_unassigned_or_unused_modifier_modreverse -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_find_swift +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend.internal". +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target demo_unassigned_or_unused_modifier_modreverse +Scanning dependencies of target demo_unassigned_or_unused_index_find_stringset +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_unassigned_or_unused_index_lcp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend.internal". +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -63489,6 +63561,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_unassigned_or_unused_index_find +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -63608,15 +63686,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -63699,6 +63768,15 @@ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_supermaxrepeats.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] @@ -63707,30 +63785,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -63811,11 +63865,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_sufarray.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -63837,7 +63908,16 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_sufarray.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -63847,6 +63927,31 @@ | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -63870,6 +63975,50 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > >; TSource = seqan::Index > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > >; TValue2 = seqan::Index > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > >; typename seqan::Reference > >::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:16:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > >& seqan::Index > >::operator=(const seqan::Index > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' + 429 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram > >; TSource = seqan::Index >, seqan::IndexQGram > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram > >; TValue2 = seqan::Index >, seqan::IndexQGram > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_qgram.h:75:33: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, QGramFindLookup) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::QGramFindLookup = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:28:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram > >& seqan::Index >, seqan::IndexQGram > >::operator=(const seqan::Index >, seqan::IndexQGram > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:91, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index >, seqan::IndexQGram > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::String >; TShapeSpec = seqan::UngappedShape<2>; TSpec = seqan::Tag]' + 278 | Index(Index const &other): + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -63891,6 +64040,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 25%] Linking CXX executable ../../bin/test_seq_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seq_io.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seq_io.dir/test_seq_io.cpp.o -o ../../bin/test_seq_io -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': @@ -63917,9 +64069,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 25%] Linking CXX executable ../../bin/test_store -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_store.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_store.dir/test_store.cpp.o -o ../../bin/test_store -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -63968,8 +64117,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': @@ -63996,7 +64143,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/unassigned_or_unused/tutorial_file_io/solution1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_solution1 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > > >; TSource = seqan::Index > > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > > >; TValue2 = seqan::Index > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > > >; typename seqan::Reference > >::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:23:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > > >& seqan::Index > > >::operator=(const seqan::Index > > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' + 429 | Index(Index const &other): + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': @@ -64043,6 +64211,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::UngappedShape<11>]' 143 | Index(Index const &other): | ^~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_seq_io +make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake --color= +[ 25%] Linking CXX executable ../../bin/test_vcf_io +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_vcf_io.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:37: @@ -64124,6 +64301,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_vcf_io.dir/test_vcf_io.cpp.o -o ../../bin/test_vcf_io -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/cigar.h:209:39: required from 'unsigned int seqan::getMDString(TMDString&, TGaps1&, TGaps2&) [with TMDString = seqan::String >; TGaps1 = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGaps2 = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::ModView > > >, seqan::Tag >, seqan::AnchorGaps > > >]' @@ -64186,6 +64364,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_unassigned_or_unused_graph_hmm_silent +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/unassigned_or_unused/graph_hmm_silent.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/unassigned_or_unused/graph_hmm_silent.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/graph_hmm_silent.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/minimapper.cpp:35: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': @@ -64361,6 +64545,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target test_vcf_io +make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_find_wild +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/unassigned_or_unused/find_wild.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_find_wild.dir/unassigned_or_unused/find_wild.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/find_wild.cpp +[ 25%] Linking CXX executable ../../bin/test_sequence +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence.dir/test_sequence.cpp.o -o ../../bin/test_sequence -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:169:56: required from 'typename seqan::Source > > >::Type seqan::source(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Source > > >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:193:24: required from 'typename seqan::GetValue > > >::Type seqan::getValue(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::GetValue > > >::Type = seqan::ModifiedAlphabet, seqan::ModExpand<'-'> >]' @@ -64423,157 +64623,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorial_file_io_solution1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_index_lcp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_store -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_index_find_stringset -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp -[ 25%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_sufarray -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o -o ../bin/demo_unassigned_or_unused_index_sufarray -lrt -lz -lbz2 [ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_supermaxrepeats cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/unassigned_or_unused/index_supermaxrepeats.cpp.o -o ../bin/demo_unassigned_or_unused_index_supermaxrepeats -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_index_sufarray -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake --color= +[ 26%] Built target test_sequence +make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend [ 26%] Built target demo_unassigned_or_unused_index_supermaxrepeats -make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend.internal". make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_graph_hmm_silent -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build -Scanning dependencies of target demo_unassigned_or_unused_index_find +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_filter_sam make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build +Scanning dependencies of target demo_unassigned_or_unused_soft_to_hard_masking +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/unassigned_or_unused/graph_hmm_silent.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/unassigned_or_unused/graph_hmm_silent.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/graph_hmm_silent.cpp -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > > >; TSource = seqan::Index > > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > > >; TValue2 = seqan::Index > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > > >; typename seqan::Reference > >::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:23:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > > >& seqan::Index > > >::operator=(const seqan::Index > > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' - 429 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > >; TSource = seqan::Index > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > >; TValue2 = seqan::Index > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > >; typename seqan::Reference > >::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:16:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > >& seqan::Index > >::operator=(const seqan::Index > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' - 429 | Index(Index const &other): - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram > >; TSource = seqan::Index >, seqan::IndexQGram > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram > >; TValue2 = seqan::Index >, seqan::IndexQGram > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_qgram.h:75:33: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, QGramFindLookup) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::QGramFindLookup = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::IndexQGram >; TSpecFinder = const seqan::Tag; TPattern = char [3]]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:28:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram > >& seqan::Index >, seqan::IndexQGram > >::operator=(const seqan::Index >, seqan::IndexQGram > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:91, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram.h:278:5: note: because 'seqan::Index >, seqan::IndexQGram > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText_ = seqan::String >; TShapeSpec = seqan::UngappedShape<2>; TSpec = seqan::Tag]' - 278 | Index(Index const &other): - | ^~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_sufarray +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/unassigned_or_unused/index_sufarray.cpp.o -o ../bin/demo_unassigned_or_unused_index_sufarray -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: @@ -64599,6 +64680,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_unassigned_or_unused_index_sufarray +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_file_format +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: @@ -64920,6 +65014,32 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:60:21: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:23:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' @@ -64972,32 +65092,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:60:21: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]; seqan::FinderMlr = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [3]]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:23:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: @@ -65134,116 +65228,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:23:34: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:23:34: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: @@ -65354,6 +65338,61 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:23:34: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' @@ -65433,6 +65472,61 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: required from 'void seqan::createSuffixArray(TSA&, const TText&, const TAlgSpec&) [with TSA = seqan::String >, seqan::Alloc<> >; TText = seqan::StringSet > >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:23:34: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_lcp.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: @@ -65758,6 +65852,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_find +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_find.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o -o ../bin/demo_unassigned_or_unused_index_find -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: @@ -65813,6 +65910,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_unassigned_or_unused_index_find +make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_find_stringset.cpp:3: @@ -65868,42 +65972,432 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_find -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_find.dir/link.txt --verbose=1 +Scanning dependencies of target demo_unassigned_or_unused_bamutil +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp [ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_graph_hmm_silent cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_find.dir/unassigned_or_unused/index_find.cpp.o -o ../bin/demo_unassigned_or_unused_index_find -lrt -lz -lbz2 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/unassigned_or_unused/graph_hmm_silent.cpp.o -o ../bin/demo_unassigned_or_unused_graph_hmm_silent -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_index_find -make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 26%] Built target demo_unassigned_or_unused_graph_hmm_silent -make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend -Scanning dependencies of target demo_unassigned_or_unused_find_wild -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend.internal". -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/unassigned_or_unused/find_wild.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_find_wild.dir/unassigned_or_unused/find_wild.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/find_wild.cpp -Scanning dependencies of target demo_unassigned_or_unused_filter_sam +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_unassigned_or_unused_bam_library_size make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_library_size.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 26%] Linking CXX executable ../../bin/test_translation +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_translation.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_translation.dir/test_translation.cpp.o -o ../../bin/test_translation -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ [ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_find_wild cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_find_wild.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_find_wild.dir/unassigned_or_unused/find_wild.cpp.o -o ../bin/demo_unassigned_or_unused_find_wild -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_unassigned_or_unused_find_wild +make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_arg_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/arg_align.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target test_translation +make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_annotation_converter +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/annotation_converter.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:18: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -65927,19 +66421,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_find_wild -make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_soft_to_hard_masking -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:18: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -66061,6 +66542,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 26%] Linking CXX executable ../../bin/test_stream +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_stream.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_stream.dir/test_stream.cpp.o -o ../../bin/test_stream -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:18: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': @@ -66260,6 +66744,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target test_stream +make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend.internal". +Scanning dependencies of target demo_tutorial_workflows_knime_node +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:17: @@ -66304,6 +66799,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/workflows/knime_node.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:17: @@ -66441,6 +66938,28 @@ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/filter_sam.cpp:18: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' @@ -66550,6 +67069,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -66583,486 +67125,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:52:15: required from 'void convertToHardMasked(TStream&, const char*) [with TStream = std::basic_ostream]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:82:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/soft_to_hard_masking.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_minimapper -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_minimapper.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_minimapper.dir/unassigned_or_unused/minimapper.cpp.o -o ../bin/demo_unassigned_or_unused_minimapper -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_minimapper -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_file_format -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:32:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:6: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_format.cpp:7: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_soft_to_hard_masking -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o -o ../bin/demo_unassigned_or_unused_soft_to_hard_masking -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_soft_to_hard_masking -make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_bamutil -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp -[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_lcp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o -o ../bin/demo_unassigned_or_unused_index_lcp -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Built target demo_unassigned_or_unused_index_lcp -make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_bam_library_size -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 26%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_library_size.cpp -[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_find_stringset -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o -o ../bin/demo_unassigned_or_unused_index_find_stringset -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_index_find_stringset -make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_arg_align -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/arg_align.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bamutil.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -67142,22 +67204,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_format -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_format.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o -o ../bin/demo_unassigned_or_unused_file_format -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_file_format -make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_annotation_converter -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/annotation_converter.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -67416,57 +67462,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_arg_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_arg_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o -o ../bin/demo_unassigned_or_unused_arg_align -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_arg_align -make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend.internal". -Scanning dependencies of target demo_tutorial_workflows_knime_node -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/workflows/knime_node.cpp -[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_bam_library_size -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o -o ../bin/demo_unassigned_or_unused_bam_library_size -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_bam_library_size -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_vcf_io_solution3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution3.cpp -[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_sam2svg -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o -o ../bin/demo_unassigned_or_unused_sam2svg -lrt -lz -lbz2 -[ 27%] Linking CXX executable ../../bin/test_stringset_v2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_stringset_v2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o -o ../../bin/test_stringset_v2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_sam2svg -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_vcf_io_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/workflows/knime_node.cpp:3: @@ -67582,6 +67577,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_soft_to_hard_masking +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/unassigned_or_unused/soft_to_hard_masking.cpp.o -o ../bin/demo_unassigned_or_unused_soft_to_hard_masking -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/workflows/knime_node.cpp:3: @@ -67658,12 +67656,50 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target test_stringset_v2 +[ 26%] Built target demo_unassigned_or_unused_soft_to_hard_masking +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend.internal". +Scanning dependencies of target demo_tutorial_vcf_io_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution3.cpp +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_arg_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_arg_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_arg_align.dir/unassigned_or_unused/arg_align.cpp.o -o ../bin/demo_unassigned_or_unused_arg_align -lrt -lz -lbz2 +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_format +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_format.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_format.dir/unassigned_or_unused/file_format.cpp.o -o ../bin/demo_unassigned_or_unused_file_format -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_unassigned_or_unused_arg_align +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend.internal". +[ 26%] Built target demo_unassigned_or_unused_file_format make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/depend +Scanning dependencies of target demo_tutorial_vcf_io_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution2.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/depend.internal". +Scanning dependencies of target demo_tutorial_string_sets_example_iterators +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/tutorial/string_sets/example_iterators.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/tutorial/string_sets/example_iterators.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/example_iterators.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution2.cpp:1: @@ -67688,12 +67724,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_string_sets_example_iterators -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/tutorial/string_sets/example_iterators.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/tutorial/string_sets/example_iterators.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/example_iterators.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, @@ -67714,14 +67744,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 29%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o -o ../bin/demo_tutorial_vcf_io_solution3 -lrt -lz -lbz2 -[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_example_iterators +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_bam_library_size +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/unassigned_or_unused/bam_library_size.cpp.o -o ../bin/demo_unassigned_or_unused_bam_library_size -lrt -lz -lbz2 +[ 26%] Linking CXX executable ../bin/demo_tutorial_string_sets_example_iterators cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/tutorial/string_sets/example_iterators.cpp.o -o ../bin/demo_tutorial_string_sets_example_iterators -lrt -lz -lbz2 -[ 29%] Built target demo_tutorial_vcf_io_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_tutorial_string_sets_example_iterators make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_base.dir/DependInfo.cmake --color= @@ -67731,10 +67761,10 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_base.dir/tutorial/string_sets/base.cpp.o +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_base.dir/tutorial/string_sets/base.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_base.dir/tutorial/string_sets/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/base.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_example_iterators +[ 26%] Built target demo_unassigned_or_unused_bam_library_size make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/DependInfo.cmake --color= @@ -67744,13 +67774,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/tutorial/string_sets/assignment_3_workshop_solution.cpp.o +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/tutorial/string_sets/assignment_3_workshop_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/tutorial/string_sets/assignment_3_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_3_workshop_solution.cpp -[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_base.dir/tutorial/string_sets/base.cpp.o -o ../bin/demo_tutorial_string_sets_base -lrt -lz -lbz2 +[ 26%] Linking CXX executable ../bin/demo_unassigned_or_unused_minimapper +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_minimapper.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_minimapper.dir/unassigned_or_unused/minimapper.cpp.o -o ../bin/demo_unassigned_or_unused_minimapper -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_base +[ 26%] Built target demo_unassigned_or_unused_minimapper make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/DependInfo.cmake --color= @@ -67760,45 +67790,45 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/tutorial/string_sets/assignment_2_solution.cpp.o +[ 26%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/tutorial/string_sets/assignment_2_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/tutorial/string_sets/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_2_solution.cpp -[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_3_workshop_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/link.txt --verbose=1 -[ 29%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o -o ../bin/demo_tutorial_vcf_io_solution2 -lrt -lz -lbz2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/tutorial/string_sets/assignment_3_workshop_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_3_workshop_solution -lrt -lz -lbz2 +[ 26%] Linking CXX executable ../bin/demo_tutorial_string_sets_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_base.dir/tutorial/string_sets/base.cpp.o -o ../bin/demo_tutorial_string_sets_base -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_assignment_3_workshop_solution +[ 26%] Built target demo_tutorial_string_sets_base make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/DependInfo.cmake --color= +[ 27%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution3.dir/link.txt --verbose=1 Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_vcf_io_solution2 -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution3.dir/tutorial/vcf_io/solution3.cpp.o -o ../bin/demo_tutorial_vcf_io_solution3 -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_string_sets_assignment_1_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/DependInfo.cmake --color= +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_1_solution.cpp +[ 27%] Linking CXX executable ../../bin/test_store +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_store.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_store.dir/test_store.cpp.o -o ../../bin/test_store -lrt -lz -lbz2 +[ 27%] Built target demo_tutorial_vcf_io_solution3 +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend.internal". -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_1_solution.cpp Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/tutorial/simple_rna_seq/genequant_solution2.cpp.o +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/tutorial/simple_rna_seq/genequant_solution2.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/tutorial/simple_rna_seq/genequant_solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution2.cpp -[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_2_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/tutorial/string_sets/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_2_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_assignment_2_solution +[ 27%] Built target test_store make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/DependInfo.cmake --color= @@ -67808,13 +67838,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/tutorial/simple_rna_seq/genequant_assignment5.cpp.o +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/tutorial/simple_rna_seq/genequant_assignment5.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/tutorial/simple_rna_seq/genequant_assignment5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp -[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_1_solution -lrt -lz -lbz2 +[ 27%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_3_workshop_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/tutorial/string_sets/assignment_3_workshop_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_3_workshop_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_assignment_1_solution +[ 27%] Built target demo_tutorial_string_sets_assignment_3_workshop_solution make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/DependInfo.cmake --color= @@ -67824,8 +67854,104 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/tutorial/simple_rna_seq/genequant_assignment4.cpp.o +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/tutorial/simple_rna_seq/genequant_assignment4.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/tutorial/simple_rna_seq/genequant_assignment4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp +[ 27%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution2.dir/tutorial/vcf_io/solution2.cpp.o -o ../bin/demo_tutorial_vcf_io_solution2 -lrt -lz -lbz2 +[ 27%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_lcp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/unassigned_or_unused/index_lcp.cpp.o -o ../bin/demo_unassigned_or_unused_index_lcp -lrt -lz -lbz2 +[ 27%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/tutorial/string_sets/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_2_solution -lrt -lz -lbz2 +[ 27%] Built target demo_tutorial_vcf_io_solution2 +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 27%] Built target demo_tutorial_string_sets_assignment_2_solution +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend +[ 27%] Built target demo_unassigned_or_unused_index_lcp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_in_depth_example_overflow +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/example_overflow.cpp +Scanning dependencies of target demo_tutorial_sequences_in_depth_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 27%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/base.cpp +[ 29%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_find_stringset +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/unassigned_or_unused/index_find_stringset.cpp.o -o ../bin/demo_unassigned_or_unused_index_find_stringset -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_unassigned_or_unused_index_find_stringset +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_index_mums +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp +[ 29%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/tutorial/string_sets/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_1_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_tutorial_string_sets_assignment_1_solution +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp +[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_base -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_tutorial_sequences_in_depth_base +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_functionality2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -67955,6 +68081,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_example_overflow +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_example_overflow -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution2.cpp:2: @@ -67981,6 +68110,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -68031,9 +68161,34 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 29%] Linking CXX executable ../../bin/test_seeds_align_banded_chain_impl -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_align_banded_chain_impl.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o -o ../../bin/test_seeds_align_banded_chain_impl -lrt -lz -lbz2 +[ 29%] Built target demo_tutorial_sequences_in_depth_example_overflow +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_functionality1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/link.txt --verbose=1 +[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/tutorial/sequences/example_functionality1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/tutorial/sequences/example_functionality1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_conversions_move +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, @@ -68112,25 +68267,52 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:40:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:36:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -68139,7 +68321,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -68151,14 +68333,14 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -68167,32 +68349,32 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:40:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:36:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -68205,161 +68387,52 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target test_seeds_align_banded_chain_impl -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:39:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:40:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 29%] Linking CXX executable ../bin/demo_unassigned_or_unused_filter_sam -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -68371,49 +68444,48 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o -o ../bin/demo_unassigned_or_unused_filter_sam -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:39:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:40:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -68426,14 +68498,13 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -68444,7 +68515,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ @@ -68457,22 +68528,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -[ 29%] Built target demo_unassigned_or_unused_filter_sam -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_in_depth_example_overflow -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/example_overflow.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' @@ -68484,20 +68543,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' @@ -68509,25 +68568,102 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_example_overflow -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/tutorial/sequences_in_depth/example_overflow.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_example_overflow -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:22:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -68538,50 +68674,126 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:36:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:39:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:35:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -68593,55 +68805,48 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:36:60: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:39:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 29%] Built target demo_tutorial_sequences_in_depth_example_overflow -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -68654,19 +68859,79 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target demo_tutorial_sequences_in_depth_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -68677,7 +68942,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ @@ -68693,7 +68958,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' @@ -68705,20 +68970,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' @@ -68730,153 +68995,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:34:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/tutorial/sequences_in_depth/base.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_base -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_sequences_in_depth_base -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_index_mums -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp -[ 29%] Linking CXX executable ../bin/demo_unassigned_or_unused_bamutil -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bamutil.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o -o ../bin/demo_unassigned_or_unused_bamutil -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_unassigned_or_unused_bamutil -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:22:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:41:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 29%] Linking CXX executable ../bin/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/tutorial/sequences_in_depth/assignment_exact_generous_solution.cpp.o -o ../bin/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_example_functionality2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: @@ -69309,6 +69437,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: @@ -69418,6 +69570,48 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: @@ -69473,6 +69667,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_mums.cpp:3: @@ -69528,49 +69746,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 29%] Linking CXX executable ../bin/demo_unassigned_or_unused_annotation_converter -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o -o ../bin/demo_unassigned_or_unused_annotation_converter -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_unassigned_or_unused_annotation_converter -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_example_functionality1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/tutorial/sequences/example_functionality1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/tutorial/sequences/example_functionality1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -69581,7 +69759,7 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -69589,12 +69767,15 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 30%] Linking CXX executable ../bin/demo_tutorial_sequences_example_functionality2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o -o ../bin/demo_tutorial_sequences_example_functionality2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -69606,55 +69787,12 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 30%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/tutorial/simple_rna_seq/genequant_solution2.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution2 -lrt -lz -lbz2 -[ 31%] Linking CXX executable ../bin/demo_tutorial_sequences_example_functionality2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/tutorial/sequences/example_functionality2.cpp.o -o ../bin/demo_tutorial_sequences_example_functionality2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Built target demo_tutorial_simple_rna_seq_genequant_solution2 -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_example_conversions_move -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp -[ 31%] Built target demo_tutorial_sequences_example_functionality2 +[ 30%] Built target demo_tutorial_sequences_example_functionality2 make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/DependInfo.cmake --color= @@ -69664,55 +69802,16 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/tutorial/sequences/assignment_6_solution.cpp.o +[ 30%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/tutorial/sequences/assignment_6_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/tutorial/sequences/assignment_6_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_6_solution.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_functionality1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 31%] Linking CXX executable ../bin/demo_tutorial_sequences_example_functionality1 +[ 30%] Linking CXX executable ../bin/demo_tutorial_sequences_example_conversions_move +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o -o ../bin/demo_tutorial_sequences_example_conversions_move -lrt -lz -lbz2 +[ 30%] Linking CXX executable ../bin/demo_tutorial_sequences_example_functionality1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/tutorial/sequences/example_functionality1.cpp.o -o ../bin/demo_tutorial_sequences_example_functionality1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Built target demo_tutorial_sequences_example_functionality1 +[ 30%] Built target demo_tutorial_sequences_example_conversions_move make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/DependInfo.cmake --color= @@ -69722,13 +69821,10 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/tutorial/sequences/assignment_5_solution.cpp.o +[ 30%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/tutorial/sequences/assignment_5_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/tutorial/sequences/assignment_5_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_5_solution.cpp -[ 31%] Linking CXX executable ../bin/demo_tutorial_workflows_knime_node -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_workflows_knime_node.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o -o ../bin/demo_tutorial_workflows_knime_node -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Built target demo_tutorial_workflows_knime_node +[ 30%] Built target demo_tutorial_sequences_example_functionality1 make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/DependInfo.cmake --color= @@ -69738,146 +69834,77 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/tutorial/sequences/assignment_3_solution.cpp.o +[ 30%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/tutorial/sequences/assignment_3_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/tutorial/sequences/assignment_3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_3_solution.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_move.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 32%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_6_solution +[ 31%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_6_solution cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/tutorial/sequences/assignment_6_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_6_solution -lrt -lz -lbz2 +[ 31%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/tutorial/sequences/assignment_3_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_3_solution -lrt -lz -lbz2 +[ 31%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_5_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/tutorial/sequences/assignment_5_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_5_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 32%] Built target demo_tutorial_sequences_assignment_6_solution +[ 31%] Built target demo_tutorial_sequences_assignment_6_solution make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_count_characters make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 32%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/count_characters.cpp -[ 32%] Linking CXX executable ../bin/demo_tutorial_sequences_example_conversions_move -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/tutorial/sequences/example_conversions_move.cpp.o -o ../bin/demo_tutorial_sequences_example_conversions_move -lrt -lz -lbz2 -[ 32%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_5_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/tutorial/sequences/assignment_5_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_5_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 32%] Built target demo_tutorial_sequences_example_conversions_move +[ 31%] Built target demo_tutorial_sequences_assignment_3_solution make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 31%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/count_characters.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_assignment_1_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 32%] Built target demo_tutorial_sequences_assignment_5_solution +[ 31%] Built target demo_tutorial_sequences_assignment_5_solution make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/DependInfo.cmake --color= -[ 32%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_1_solution.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_assignment_1_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_1_solution.cpp Scanning dependencies of target demo_tutorial_sequence_io_solution2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 32%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/tutorial/sequence_io/solution2.cpp.o +[ 31%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/tutorial/sequence_io/solution2.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution2.dir/tutorial/sequence_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution2.cpp -[ 33%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_count_characters -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_count_characters -lrt -lz -lbz2 +[ 31%] Linking CXX executable ../bin/demo_unassigned_or_unused_sam2svg +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/unassigned_or_unused/sam2svg.cpp.o -o ../bin/demo_unassigned_or_unused_sam2svg -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 33%] Built target demo_unassigned_or_unused_tutorial_sequence_count_characters +[ 31%] Built target demo_unassigned_or_unused_sam2svg make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/depend.internal". -[ 33%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/link.txt --verbose=1 Scanning dependencies of target demo_tutorial_sequence_io_example1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/tutorial/simple_rna_seq/genequant_assignment5.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment5 -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 34%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/tutorial/sequence_io/example1.cpp.o +[ 32%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/tutorial/sequence_io/example1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_example1.dir/tutorial/sequence_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp -[ 34%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_3_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/tutorial/sequences/assignment_3_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_3_solution -lrt -lz -lbz2 +[ 33%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_count_characters +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/unassigned_or_unused/tutorial_sequence/count_characters.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_count_characters -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 34%] Built target demo_tutorial_sequences_assignment_3_solution +[ 33%] Built target demo_unassigned_or_unused_tutorial_sequence_count_characters make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/DependInfo.cmake --color= @@ -69887,69 +69914,24 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 34%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/tutorial/sequence_io/base.cpp.o +[ 33%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/tutorial/sequence_io/base.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_base.dir/tutorial/sequence_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp -[ 34%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/link.txt --verbose=1 +[ 34%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_1_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 34%] Built target demo_tutorial_simple_rna_seq_genequant_assignment5 +[ 34%] Built target demo_tutorial_sequences_assignment_1_solution make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment2 -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/depend.internal". -[ 35%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/tutorial/sequences/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_1_solution -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_seeds_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/tutorial/seeds/solution1.cpp.o +[ 34%] Building CXX object demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/tutorial/seeds/solution1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seeds_solution1.dir/tutorial/seeds/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/solution1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_sequences_assignment_1_solution -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_string_sets_assignment_4_workshop_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_4_workshop_solution.cpp -[ 35%] Built target demo_tutorial_simple_rna_seq_genequant_assignment2 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/DependInfo.cmake --color= -[ 35%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/tutorial/simple_rna_seq/genequant_assignment4.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment4 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_seed_and_extend_solution6 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_simple_rna_seq_genequant_assignment4 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution2.cpp:1: @@ -70167,6 +70149,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 34%] Linking CXX executable ../bin/demo_unassigned_or_unused_bamutil +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bamutil.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bamutil.dir/unassigned_or_unused/bamutil.cpp.o -o ../bin/demo_unassigned_or_unused_bamutil -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 34%] Built target demo_unassigned_or_unused_bamutil +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_string_sets_assignment_4_workshop_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 34%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_4_workshop_solution.cpp +[ 34%] Linking CXX executable ../bin/demo_unassigned_or_unused_annotation_converter +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/unassigned_or_unused/annotation_converter.cpp.o -o ../bin/demo_unassigned_or_unused_annotation_converter -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 34%] Built target demo_unassigned_or_unused_annotation_converter +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend.internal". +Scanning dependencies of target demo_tutorial_seed_and_extend_solution6 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 34%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: @@ -70330,13 +70344,12 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:11:47: required from here + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -70344,7 +70357,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -70352,14 +70365,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' @@ -70384,24 +70397,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:13:47: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -70423,12 +70426,13 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:13:47: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:11:47: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -70436,7 +70440,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -70444,7 +70448,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/base.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/example1.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -70613,6 +70617,69 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 35%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/tutorial/simple_rna_seq/genequant_solution2.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Built target demo_tutorial_simple_rna_seq_genequant_solution2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_seed_and_extend_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution2.cpp +[ 35%] Linking CXX executable ../bin/demo_tutorial_seeds_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seeds_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seeds_solution1.dir/tutorial/seeds/solution1.cpp.o -o ../bin/demo_tutorial_seeds_solution1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Built target demo_tutorial_seeds_solution1 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend.internal". +Scanning dependencies of target demo_tutorial_seed_and_extend_example7 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp +[ 35%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/tutorial/simple_rna_seq/genequant_assignment2.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Built target demo_tutorial_simple_rna_seq_genequant_assignment2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend.internal". +Scanning dependencies of target demo_tutorial_seed_and_extend_example6 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example6.cpp +[ 35%] Linking CXX executable ../bin/demo_tutorial_workflows_knime_node +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_workflows_knime_node.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_workflows_knime_node.dir/tutorial/workflows/knime_node.cpp.o -o ../bin/demo_tutorial_workflows_knime_node -lrt -lz -lbz2 +[ 35%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_4_workshop_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] @@ -70621,6 +70688,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_4_workshop_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 35%] Built target demo_tutorial_string_sets_assignment_4_workshop_solution +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend.internal". +Scanning dependencies of target demo_tutorial_seed_and_extend_example5 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example5.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Built target demo_tutorial_workflows_knime_node +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_benchmark_stream_write +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/unassigned_or_unused/benchmark_stream_write.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/unassigned_or_unused/benchmark_stream_write.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -70737,8 +70831,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 35%] Linking CXX executable ../bin/demo_tutorial_seeds_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seeds_solution1.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -70791,7 +70883,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seeds_solution1.dir/tutorial/seeds/solution1.cpp.o -o ../bin/demo_tutorial_seeds_solution1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution2.cpp:4: @@ -70856,11 +70947,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_seeds_solution1 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': @@ -70881,11 +70967,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_example7 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution6.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': @@ -70907,44 +70988,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp -[ 35%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_4_workshop_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/tutorial/string_sets/assignment_4_workshop_solution.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_4_workshop_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_string_sets_assignment_4_workshop_solution -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_example6 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example6.cpp -[ 35%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_seed_and_extend_solution2 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_example5 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example5.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example6.cpp:4: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -70952,9 +70998,47 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/tutorial/seed_and_extend/solution2.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Built target demo_tutorial_seed_and_extend_solution2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend.internal". +[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution2.dir/tutorial/sequence_io/solution2.cpp.o -o ../bin/demo_tutorial_sequence_io_solution2 -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_seed_and_extend_example4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment5 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/link.txt --verbose=1 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/tutorial/simple_rna_seq/genequant_assignment5.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment5 -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example4.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Built target demo_tutorial_sequence_io_solution2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend.internal". +[ 36%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/tutorial/simple_rna_seq/genequant_assignment4.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment4 -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_seed_and_extend_example2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:5: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example6.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -70962,6 +71046,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Built target demo_tutorial_simple_rna_seq_genequant_assignment5 +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_q_gram_index_index_qgram_hash In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -70983,6 +71076,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -71011,6 +71105,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Built target demo_tutorial_simple_rna_seq_genequant_assignment4 +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend +[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram_hash.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend.internal". +Scanning dependencies of target demo_tutorial_q_gram_index_index_assignment6 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:509:24: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWise&) [with TDPScout = seqan::DPScout_ >, seqan::Tag >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::BandedChainAlignment_, seqan::Tag >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWise = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::StringSet >, seqan::Owner<> >; TScoutState = seqan::DPScoutState_ > > >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::BandedChainAlignment_, seqan::Tag >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' @@ -71029,6 +71136,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -71083,6 +71191,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_assignment6.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::SuffixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -71147,9 +71257,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example6 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example6 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': @@ -71206,14 +71313,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_seed_and_extend_example6 -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_benchmark_stream_write In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>]': @@ -71235,11 +71334,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 129 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/unassigned_or_unused/benchmark_stream_write.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/unassigned_or_unused/benchmark_stream_write.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example7.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': @@ -71262,54 +71356,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example5 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_seed_and_extend_example5 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_example4 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example4.cpp -[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_example1.dir/tutorial/sequence_io/example1.cpp.o -o ../bin/demo_tutorial_sequence_io_example1 -lrt -lz -lbz2 -[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution2.dir/tutorial/sequence_io/solution2.cpp.o -o ../bin/demo_tutorial_sequence_io_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_sequence_io_example1 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_example2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example2.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_sequence_io_solution2 -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend.internal". -Scanning dependencies of target demo_tutorial_q_gram_index_index_qgram_hash -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram_hash.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:47: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -71334,6 +71380,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_example1.dir/tutorial/sequence_io/example1.cpp.o -o ../bin/demo_tutorial_sequence_io_example1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream_write.cpp:47: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -71380,57 +71429,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example4.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_base.dir/tutorial/sequence_io/base.cpp.o -o ../bin/demo_tutorial_sequence_io_base -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_sequence_io_base -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend.internal". -Scanning dependencies of target demo_tutorial_q_gram_index_index_assignment6 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_assignment6.cpp -[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example4 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram_hash.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_seed_and_extend_example4 +[ 36%] Built target demo_tutorial_sequence_io_example1 make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/depend -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example2.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/depend.internal". @@ -71441,43 +71442,43 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 36%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/tutorial/q_gram_index/index_assignment5.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/tutorial/q_gram_index/index_assignment5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_assignment5.cpp -[ 36%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_mums -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_mums.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o -o ../bin/demo_unassigned_or_unused_index_mums -lrt -lz -lbz2 -[ 36%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_qgram_hash -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_qgram_hash -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/tutorial/seed_and_extend/example5.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example5 -lrt -lz -lbz2 +[ 36%] Linking CXX executable ../bin/demo_tutorial_sequence_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_base.dir/tutorial/sequence_io/base.cpp.o -o ../bin/demo_tutorial_sequence_io_base -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_unassigned_or_unused_index_mums +[ 36%] Built target demo_tutorial_seed_and_extend_example5 make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/DependInfo.cmake --color= -[ 36%] Built target demo_tutorial_q_gram_index_index_qgram_hash -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend.internal". Scanning dependencies of target demo_tutorial_pattern_matching_find_index_multiple make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 36%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example6 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/link.txt --verbose=1 +[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/tutorial/seed_and_extend/example6.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example6 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_tutorial_sequence_io_base +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend.internal". Scanning dependencies of target demo_tutorial_pattern_matching_find_exact make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build -[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp -[ 37%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/link.txt --verbose=1 [ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/tutorial/pattern_matching/find_exact.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/tutorial/pattern_matching/find_exact.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_exact.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_tutorial_seed_and_extend_example2 +[ 37%] Built target demo_tutorial_seed_and_extend_example6 make -f demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/DependInfo.cmake --color= @@ -71490,6 +71491,55 @@ [ 37%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/unassigned_or_unused/seeds.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_seeds.dir/unassigned_or_unused/seeds.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/seeds.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example4.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example2.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 37%] Linking CXX executable ../bin/demo_unassigned_or_unused_filter_sam +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/unassigned_or_unused/filter_sam.cpp.o -o ../bin/demo_unassigned_or_unused_filter_sam -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram_hash.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_unassigned_or_unused_filter_sam +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_simple +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_simple.cpp +[ 37%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/tutorial/seed_and_extend/example4.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example4 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_assignment6.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] @@ -71498,6 +71548,66 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 37%] Built target demo_tutorial_seed_and_extend_example4 +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend.internal". +Scanning dependencies of target demo_dox_index_UNUSED_shape_hash +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash.cpp +[ 37%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/tutorial/seed_and_extend/example2.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_tutorial_seed_and_extend_example2 +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake --color= +[ 37%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_mums +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_mums.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_mums.dir/unassigned_or_unused/index_mums.cpp.o -o ../bin/demo_unassigned_or_unused_index_mums -lrt -lz -lbz2 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend.internal". +[ 37%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_qgram_hash +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/link.txt --verbose=1 +Scanning dependencies of target demo_tutorial_alphabets_assignment_1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/tutorial/q_gram_index/index_qgram_hash.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_qgram_hash -lrt -lz -lbz2 +[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/assignment_1.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_tutorial_q_gram_index_index_qgram_hash +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_unassigned_or_unused_index_mums +make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend +Scanning dependencies of target demo_tutorial_a_first_example_solution_5 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend.internal". +[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_5.cpp +Scanning dependencies of target demo_tutorial_realignment_step2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_assignment5.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -71565,32 +71675,63 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 37%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_exact +[ 38%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_exact cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/link.txt --verbose=1 +[ 38%] Linking CXX executable ../bin/demo_tutorial_alphabets_assignment_1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/tutorial/pattern_matching/find_exact.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_exact -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o -o ../bin/demo_tutorial_alphabets_assignment_1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_tutorial_pattern_matching_find_exact -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend -[ 37%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_assignment5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/link.txt --verbose=1 +[ 38%] Built target demo_tutorial_pattern_matching_find_exact +make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend.internal". +Scanning dependencies of target demo_howto_filter_similar_sequences +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Building CXX object demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Built target demo_tutorial_alphabets_assignment_1 +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_file_readwrite +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp +[ 38%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_assignment5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/tutorial/q_gram_index/index_assignment5.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_assignment5 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_simple make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build +[ 38%] Built target demo_tutorial_q_gram_index_index_assignment5 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_simple.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_kruskals_algorithm make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_tutorial_q_gram_index_index_assignment5 -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend +make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend.internal". +[ 38%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/kruskals_algorithm.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -71617,12 +71758,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_dox_index_UNUSED_shape_hash -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash.cpp +[ 38%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_assignment6 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_assignment6 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -71731,6 +71869,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -71758,6 +71897,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 38%] Built target demo_tutorial_q_gram_index_index_assignment6 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -71812,6 +71957,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target demo_tutorial_a_first_example_solution_3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_3.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -72083,6 +72234,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 38%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_5 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -72137,9 +72291,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 37%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_assignment6 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/tutorial/q_gram_index/index_assignment6.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_assignment6 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Built target demo_tutorial_a_first_example_solution_5 +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -72195,6 +72351,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_index_qgram_counts +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index_multiple.cpp:3: @@ -72250,56 +72411,75 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_tutorial_q_gram_index_index_assignment6 -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alphabets_assignment_1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/assignment_1.cpp -[ 37%] Linking CXX executable ../bin/demo_unassigned_or_unused_seeds +[ 38%] Linking CXX executable ../bin/demo_unassigned_or_unused_seeds cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_seeds.dir/link.txt --verbose=1 +[ 38%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_qgram_counts.cpp +[ 38%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape_hash +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_seeds.dir/unassigned_or_unused/seeds.cpp.o -o ../bin/demo_unassigned_or_unused_seeds -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o -o ../bin/demo_dox_index_UNUSED_shape_hash -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_unassigned_or_unused_seeds -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend +[ 38%] Built target demo_dox_index_UNUSED_shape_hash +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend +[ 38%] Built target demo_unassigned_or_unused_seeds +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend.internal". -[ 37%] Linking CXX executable ../bin/demo_tutorial_alphabets_assignment_1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/tutorial/alphabets/assignment_1.cpp.o -o ../bin/demo_tutorial_alphabets_assignment_1 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_a_first_example_solution_5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend.internal". +Scanning dependencies of target demo_tutorial_genome_annotations_assignment_4_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp +Scanning dependencies of target demo_dox_index_begin_range_goDown_representative_repLength make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_5.cpp -[ 37%] Built target demo_tutorial_alphabets_assignment_1 -make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend +make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake --color= -[ 37%] Linking CXX executable ../bin/demo_unassigned_or_unused_benchmark_stream_write -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend.internal". +[ 38%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_readwrite +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/link.txt --verbose=1 +[ 38%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o -o ../bin/demo_unassigned_or_unused_file_readwrite -lrt -lz -lbz2 +[ 38%] Linking CXX executable ../bin/demo_unassigned_or_unused_benchmark_stream_write cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/unassigned_or_unused/benchmark_stream_write.cpp.o -o ../bin/demo_unassigned_or_unused_benchmark_stream_write -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_realignment_step2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build +[ 38%] Built target demo_unassigned_or_unused_file_readwrite +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 38%] Built target demo_unassigned_or_unused_benchmark_stream_write +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/DependInfo.cmake --color= +[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_own_function +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_own_function.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -72307,37 +72487,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_unassigned_or_unused_benchmark_stream_write -make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend.internal". -Scanning dependencies of target demo_howto_filter_similar_sequences -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp -[ 38%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape_hash -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/dox/index/UNUSED_shape_hash.cpp.o -o ../bin/demo_dox_index_UNUSED_shape_hash -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_dox_index_UNUSED_shape_hash -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_file_readwrite -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_readwrite.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:3: + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -72345,38 +72499,44 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 38%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/tutorial/a_first_example/solution_5.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_5 -lrt -lz -lbz2 +[ 39%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_tutorial_a_first_example_solution_5 -make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend +[ 39%] Linking CXX executable ../bin/demo_dox_graph_algorithms_kruskals_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/link.txt --verbose=1 +[ 39%] Built target demo_tutorial_a_first_example_solution_3 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_kruskals_algorithm -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_kruskals_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_solution_2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/kruskals_algorithm.cpp -[ 38%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_readwrite -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/unassigned_or_unused/file_readwrite.cpp.o -o ../bin/demo_unassigned_or_unused_file_readwrite -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_unassigned_or_unused_file_readwrite -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend +[ 39%] Built target demo_dox_graph_algorithms_kruskals_algorithm +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_solution_3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake --color= +[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_2.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_solution_1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_3.cpp +[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/tutorial/a_first_example/solution_1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/tutorial/a_first_example/solution_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_1.cpp +[ 39%] Linking CXX executable ../../bin/test_stringset_v2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_stringset_v2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_stringset_v2.dir/test_stringset_v2.cpp.o -o ../../bin/test_stringset_v2 -lrt -lz -lbz2 +[ 39%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_simple +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_simple -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, @@ -72394,6 +72554,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 39%] Built target demo_tutorial_alignment_scoring_scheme_simple +make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_code_encapsulation In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -72436,6 +72604,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/code_encapsulation.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -72526,9 +72699,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 38%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_simple -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/tutorial/alignment/scoring_scheme_simple.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_simple -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 39%] Built target test_stringset_v2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -72554,18 +72731,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +Scanning dependencies of target demo_tutorial_seed_and_extend_example3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:28:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': @@ -72611,100 +72799,58 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example3.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_qgram_counts.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 38%] Built target demo_tutorial_alignment_scoring_scheme_simple -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/DependInfo.cmake --color= -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1261:14: required from 'bool seqan::loadReads(seqan::FragmentStore&, TFileName&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TFileName = const char*]' -/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:14:50: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1875:33: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:35:41: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1261:14: required from 'bool seqan::loadReads(seqan::FragmentStore&, TFileName&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TFileName = const char*]' -/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:14:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -72712,21 +72858,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_unassigned_or_unused_index_qgram_counts -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' @@ -72749,32 +72884,53 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:740:41: required from 'void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1875:33: required from 'bool seqan::_firstNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1934:34: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' /build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = void]' /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:35:41: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<11> >]' - 143 | Index(Index const &other): - | ^~~~~ -[ 38%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_qgram_counts.cpp +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:22:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -72798,68 +72954,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:28:72: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:22:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' @@ -72925,6 +73019,62 @@ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1261:14: required from 'bool seqan::loadReads(seqan::FragmentStore&, TFileName&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TFileName = const char*]' +/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:14:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSource = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_pattern_base.h:339:17: required from 'typename seqan::Host >::Type& seqan::host(seqan::Pattern&) [with TNeedle = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Swift > >; typename seqan::Host >::Type = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:740:41: required from 'void seqan::_patternInit(seqan::Pattern >&, TFloat, TSize_) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TFloat = double; TSize_ = int; TSpec = seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1929:21: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double, TSize) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = seqan::Tag >; TSize = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_swift.h:1913:16: required from 'bool seqan::find(TFinder&, seqan::Pattern > > >&, double) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Swift > > >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:35:41: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Owner > >, seqan::IndexQGram, seqan::UngappedShape<11> >, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >; TShapeSpec = seqan::Shape, seqan::UngappedShape<11> >]' + 143 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, @@ -72952,6 +73102,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1261:14: required from 'bool seqan::loadReads(seqan::FragmentStore&, TFileName&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TFileName = const char*]' +/build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:14:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/filter_similar_sequences.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -73087,6 +73263,83 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:18:14: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:18:14: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -73117,6 +73370,150 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDownChar(seqan::Iter > >&, TValue) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TValue = char]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1928:27: required from 'bool seqan::_goDownString(seqan::Iter > >&, const TString&, TSize&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TString = char [5]; TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1974:29: required from 'bool seqan::_goDownObject(seqan::Iter > >&, const TObject&, seqan::True) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1985:29: required from 'bool seqan::goDown(seqan::Iter > >&, const TObject&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:12:22: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1898:23: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1898 | value(it) = nodeDesc; + | ~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 235 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 253 | finger2 = col_; //points to last column + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 255 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 595 | it_ = source_; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 445 | finger1 = end_col; //points to last column + | ~~~~~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 447 | finger0 = end_col; + | ~~~~~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1897:25: required from 'bool seqan::_goDownChar(seqan::Iter > >&, TValue) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TValue = char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1928:27: required from 'bool seqan::_goDownString(seqan::Iter > >&, const TString&, TSize&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TString = char [5]; TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1974:29: required from 'bool seqan::_goDownObject(seqan::Iter > >&, const TObject&, seqan::True) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1985:29: required from 'bool seqan::goDown(seqan::Iter > >&, const TObject&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:12:22: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1751:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1751 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: @@ -73171,6 +73568,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -73192,6 +73609,129 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -73254,6 +73794,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: @@ -73306,6 +73868,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:11:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: @@ -73362,6 +73946,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step2.cpp:1: @@ -73443,6 +74050,46 @@ 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:11:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, @@ -73473,8 +74120,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 38%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -73500,21 +74145,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/tutorial/a_first_example/solution_3.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_3 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_qgram_counts.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_tutorial_a_first_example_solution_3 -make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -73548,604 +74178,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend.internal". -Scanning dependencies of target demo_dox_index_begin_range_goDown_representative_repLength -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build -[ 38%] Linking CXX executable ../bin/demo_dox_graph_algorithms_kruskals_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/dox/graph_algorithms/kruskals_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_kruskals_algorithm -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_dox_graph_algorithms_kruskals_algorithm -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_genome_annotations_assignment_4_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp -[ 38%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_qgram_counts -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o -o ../bin/demo_unassigned_or_unused_index_qgram_counts -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_unassigned_or_unused_index_qgram_counts -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:18:14: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:18:14: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDownChar(seqan::Iter > >&, TValue) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TValue = char]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1928:27: required from 'bool seqan::_goDownString(seqan::Iter > >&, const TString&, TSize&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TString = char [5]; TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1974:29: required from 'bool seqan::_goDownObject(seqan::Iter > >&, const TObject&, seqan::True) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1985:29: required from 'bool seqan::goDown(seqan::Iter > >&, const TObject&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:12:22: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1898:23: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1898 | value(it) = nodeDesc; - | ~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1897:25: required from 'bool seqan::_goDownChar(seqan::Iter > >&, TValue) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TValue = char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1928:27: required from 'bool seqan::_goDownString(seqan::Iter > >&, const TString&, TSize&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TString = char [5]; TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1974:29: required from 'bool seqan::_goDownObject(seqan::Iter > >&, const TObject&, seqan::True) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1985:29: required from 'bool seqan::goDown(seqan::Iter > >&, const TObject&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; TObject = char [5]]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:12:22: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1751:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1751 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:13:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_range_goDown_representative_repLength.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:11:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:11:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_4_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 235 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 253 | finger2 = col_; //points to last column - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 255 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 595 | it_ = source_; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 445 | finger1 = end_col; //points to last column - | ~~~~~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 447 | finger0 = end_col; - | ~~~~~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 38%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution6 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution6 -lrt -lz -lbz2 -[ 38%] Linking CXX executable ../bin/demo_dox_index_begin_range_goDown_representative_repLength -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o -o ../bin/demo_dox_index_begin_range_goDown_representative_repLength -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Built target demo_tutorial_seed_and_extend_solution6 -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/DependInfo.cmake --color= -[ 38%] Built target demo_dox_index_begin_range_goDown_representative_repLength -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend.internal". -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_solution_2 -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_own_function -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 38%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o -[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_own_function.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_2.cpp -[ 39%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_solution_1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/tutorial/a_first_example/solution_1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/tutorial/a_first_example/solution_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_1.cpp -[ 39%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Built target demo_tutorial_a_first_example_solution_2 -make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_code_encapsulation -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/code_encapsulation.cpp -[ 39%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example7 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example7 -lrt -lz -lbz2 [ 39%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/tutorial/a_first_example/solution_1.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Built target demo_tutorial_seed_and_extend_example7 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 39%] Built target demo_tutorial_a_first_example_solution_1 make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' @@ -74155,28 +74191,22 @@ Scanning dependencies of target demo_dox_misc_get_terminal_size make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build -[ 39%] Linking CXX executable ../bin/demo_howto_filter_similar_sequences -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_filter_similar_sequences.dir/link.txt --verbose=1 -Scanning dependencies of target demo_tutorial_seed_and_extend_example3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o -o ../bin/demo_howto_filter_similar_sequences -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 39%] Building CXX object demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/dox/misc/get_terminal_size.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_get_terminal_size.dir/dox/misc/get_terminal_size.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/get_terminal_size.cpp -[ 39%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example3.cpp -[ 39%] Linking CXX executable ../bin/demo_dox_misc_get_terminal_size -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_get_terminal_size.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_get_terminal_size.dir/dox/misc/get_terminal_size.cpp.o -o ../bin/demo_dox_misc_get_terminal_size -lrt -lz -lbz2 +[ 39%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/tutorial/a_first_example/solution_2.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Built target demo_howto_filter_similar_sequences +[ 39%] Built target demo_tutorial_a_first_example_solution_2 make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/DependInfo.cmake --color= +[ 39%] Linking CXX executable ../bin/demo_dox_misc_get_terminal_size +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_get_terminal_size.dir/link.txt --verbose=1 Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/depend.internal". +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_get_terminal_size.dir/dox/misc/get_terminal_size.cpp.o -o ../bin/demo_dox_misc_get_terminal_size -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_seed_and_extend_solution4 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build @@ -74196,11 +74226,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/tutorial/a_first_example/basic_code.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/tutorial/a_first_example/basic_code.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/basic_code.cpp -[ 40%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_4_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_4_solution -lrt -lz -lbz2 +[ 40%] Linking CXX executable ../bin/demo_tutorial_a_first_example_code_encapsulation +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o -o ../bin/demo_tutorial_a_first_example_code_encapsulation -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_genome_annotations_assignment_4_solution +[ 40%] Built target demo_tutorial_a_first_example_code_encapsulation make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/DependInfo.cmake --color= @@ -74210,50 +74240,44 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Linking CXX executable ../bin/demo_tutorial_a_first_example_code_encapsulation -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/link.txt --verbose=1 +[ 40%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_qgram_counts +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/link.txt --verbose=1 [ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/tutorial/vcf_io/example1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_example1.dir/tutorial/vcf_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/example1.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/tutorial/a_first_example/code_encapsulation.cpp.o -o ../bin/demo_tutorial_a_first_example_code_encapsulation -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/unassigned_or_unused/index_qgram_counts.cpp.o -o ../bin/demo_unassigned_or_unused_index_qgram_counts -lrt -lz -lbz2 +[ 40%] Linking CXX executable ../bin/demo_dox_index_begin_range_goDown_representative_repLength +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/dox/index/begin_range_goDown_representative_repLength.cpp.o -o ../bin/demo_dox_index_begin_range_goDown_representative_repLength -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_a_first_example_code_encapsulation +[ 40%] Built target demo_unassigned_or_unused_index_qgram_counts make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/depend.internal". +[ 40%] Built target demo_dox_index_begin_range_goDown_representative_repLength +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend.internal". Scanning dependencies of target demo_tutorial_consensus_alignment_with_positions make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/tutorial/consensus_alignment/with_positions.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/tutorial/consensus_alignment/with_positions.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp -[ 40%] Linking CXX executable ../bin/demo_tutorial_a_first_example_basic_code -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/tutorial/a_first_example/basic_code.cpp.o -o ../bin/demo_tutorial_a_first_example_basic_code -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_a_first_example_basic_code -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake --color= -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution4.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend.internal". Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment3 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/tutorial/journaled_set/solution_online_search_assignment3.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/tutorial/journaled_set/solution_online_search_assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment3.cpp +[ 40%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_local_assignment1.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example3.cpp:5: @@ -74264,9 +74288,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 40%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_index_multiple -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_index_multiple -lrt -lz -lbz2 +[ 40%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sam_and_bam_io_example7 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp +[ 40%] Linking CXX executable ../bin/demo_tutorial_a_first_example_basic_code +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/tutorial/a_first_example/basic_code.cpp.o -o ../bin/demo_tutorial_a_first_example_basic_code -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Built target demo_tutorial_a_first_example_basic_code +make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/example1.cpp:1: @@ -74291,6 +74334,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_tutorial_alignment_graph_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/tutorial/alignment/graph_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/tutorial/alignment/graph_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/graph_assignment1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, @@ -74311,39 +74360,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 40%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/tutorial/seed_and_extend/solution4.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution4 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_seed_and_extend_solution4 -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sam_and_bam_io_example7 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp -[ 40%] Built target demo_tutorial_pattern_matching_find_index_multiple -make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alignment_graph_assignment1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/tutorial/alignment/graph_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/tutorial/alignment/graph_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/graph_assignment1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:5: + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution4.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -74351,6 +74370,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 40%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/tutorial/seed_and_extend/solution4.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution4 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Built target demo_tutorial_seed_and_extend_solution4 +make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:44, @@ -74370,6 +74399,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_howto_efficiently_import_sequences +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Building CXX object demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment3.cpp:3: @@ -74588,6 +74623,29 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -74640,6 +74698,106 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 40%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_4_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/tutorial/genome_annotations/assignment_4_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_4_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Built target demo_tutorial_genome_annotations_assignment_4_solution +make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_alphabet +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/alphabet.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 40%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example3 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 40%] Built target demo_tutorial_seed_and_extend_example3 +make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend.internal". +Scanning dependencies of target demo_howto_custom_file_endings +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp +[ 41%] Linking CXX executable ../bin/demo_unassigned_or_unused_alphabet +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_alphabet.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o -o ../bin/demo_unassigned_or_unused_alphabet -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_unassigned_or_unused_alphabet +make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/depend.internal". +Scanning dependencies of target demo_dox_store_store_example +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:4: @@ -74819,29 +74977,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, @@ -74861,30 +74996,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:4: @@ -74904,23 +75015,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example7.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -74942,6 +75036,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +[ 41%] Linking CXX executable ../bin/demo_howto_filter_similar_sequences +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_filter_similar_sequences.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_filter_similar_sequences.dir/howto/filter_similar_sequences.cpp.o -o ../bin/demo_howto_filter_similar_sequences -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -75005,6 +75102,64 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 41%] Linking CXX executable ../bin/demo_tutorial_vcf_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_example1.dir/tutorial/vcf_io/example1.cpp.o -o ../bin/demo_tutorial_vcf_io_example1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -75026,6 +75181,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 41%] Built target demo_howto_filter_similar_sequences +make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:4: @@ -75087,6 +75244,130 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_dox_sequence_string2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/string2.cpp +[ 41%] Built target demo_tutorial_vcf_io_example1 +make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/with_positions.cpp:4: @@ -75167,6 +75448,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +Scanning dependencies of target demo_tutorial_basic_techniques_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:910:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:1006:37: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' @@ -75192,6 +75505,36 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basic_techniques/base.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, @@ -75492,8 +75835,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -[ 40%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -75587,7 +75928,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/tutorial/seed_and_extend/example3.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -75710,19 +76050,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_seed_and_extend_example3 -make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend.internal". -Scanning dependencies of target demo_howto_efficiently_import_sequences -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Building CXX object demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp +[ 41%] Linking CXX executable ../bin/demo_tutorial_basic_techniques_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basic_techniques_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o -o ../bin/demo_tutorial_basic_techniques_base -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' @@ -75752,699 +76082,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 40%] Linking CXX executable ../bin/demo_tutorial_vcf_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_example1.dir/tutorial/vcf_io/example1.cpp.o -o ../bin/demo_tutorial_vcf_io_example1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_vcf_io_example1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend +[ 41%] Built target demo_tutorial_basic_techniques_base +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_alphabet +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_bed_io_solution2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/alphabet.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:15:43: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/howto/efficiently_import_sequences.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 40%] Linking CXX executable ../bin/demo_tutorial_alignment_graph_assignment1 +[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp +[ 41%] Linking CXX executable ../bin/demo_tutorial_alignment_graph_assignment1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/tutorial/alignment/graph_assignment1.cpp.o -o ../bin/demo_tutorial_alignment_graph_assignment1 -lrt -lz -lbz2 -[ 40%] Linking CXX executable ../bin/demo_unassigned_or_unused_alphabet -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_alphabet.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_alphabet.dir/unassigned_or_unused/alphabet.cpp.o -o ../bin/demo_unassigned_or_unused_alphabet -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_alignment_graph_assignment1 -make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend.internal". -Scanning dependencies of target demo_howto_custom_file_endings -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_unassigned_or_unused_alphabet -make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/depend.internal". -Scanning dependencies of target demo_dox_store_store_example -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -76469,6 +76122,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 41%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution6 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/tutorial/seed_and_extend/solution6.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution6 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::MySeqFormat_]': @@ -76493,6 +76149,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -76518,1696 +76175,184 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 41%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_own_function -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_own_function -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_tutorial_parsing_command_line_arguments_example_with_own_function -make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_string2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/string2.cpp -[ 41%] Linking CXX executable ../bin/demo_dox_sequence_string2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_string2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o -o ../bin/demo_dox_sequence_string2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_dox_sequence_string2 -make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_basic_techniques_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basic_techniques/base.cpp -[ 41%] Linking CXX executable ../bin/demo_howto_efficiently_import_sequences -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_efficiently_import_sequences.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o -o ../bin/demo_howto_efficiently_import_sequences -lrt -lz -lbz2 -[ 41%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example7 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example7 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Linking CXX executable ../bin/demo_tutorial_basic_techniques_base -[ 41%] Built target demo_howto_efficiently_import_sequences -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basic_techniques_base.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basic_techniques_base.dir/tutorial/basic_techniques/base.cpp.o -o ../bin/demo_tutorial_basic_techniques_base -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_bed_io_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp -[ 41%] Built target demo_tutorial_sam_and_bam_io_example7 +[ 41%] Built target demo_tutorial_alignment_graph_assignment1 make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_sam_and_bam_io_example2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_tutorial_basic_techniques_base -make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend -[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake --color= -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_transitive_closure -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/transitive_closure.cpp -[ 41%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/tutorial/journaled_set/solution_online_search_assignment3.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment3 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:10:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_tutorial_journaled_set_solution_online_search_assignment3 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:10:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target demo_tutorial_seed_and_extend_example1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example1.cpp -[ 41%] Linking CXX executable ../bin/demo_tutorial_realignment_step2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_realignment_step2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o -o ../bin/demo_tutorial_realignment_step2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_tutorial_realignment_step2 -make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_segment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 41%] Linking CXX executable ../bin/demo_dox_graph_algorithms_transitive_closure -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o -o ../bin/demo_dox_graph_algorithms_transitive_closure -lrt -lz -lbz2 -[ 41%] Linking CXX executable ../bin/demo_howto_custom_file_endings -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_custom_file_endings.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o -o ../bin/demo_howto_custom_file_endings -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_dox_graph_algorithms_transitive_closure -make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_container_view_zip -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/container_view_zip.cpp -/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:93:33: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 93 | TExplicitPrefix preB(sufA, 3); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:89:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' - 89 | Segment(typename Parameter_::Type _host, typename Position::Type _end_index): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_howto_custom_file_endings -make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/DependInfo.cmake --color= -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:90:29: required from 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:93:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_depth_first_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h: In instantiation of 'typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:171:32: required from 'typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:206:53: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const seqan::Segment&, Standard) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator, const seqan::Tag >::Type = char*; seqan::Standard = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1095:69: required from 'typename seqan::EnableIf, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::SuffixSegment>, seqan::PrefixSegment>; typename seqan::EnableIf, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::PrefixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:94:18: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] - 365 | return _object; - | ^~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, - from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 129 | operator = (Segment const & source) - | ^~~~~~~~ -make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/depth_first_search.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example1.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 43%] Linking CXX executable ../bin/demo_dox_sequence_segment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_segment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o -o ../bin/demo_dox_sequence_segment -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_sequence_segment -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend.internal". -[ 43%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example1 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_indexed_fasta_io_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_seed_and_extend_example1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_segmentalignment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp -[ 43%] Linking CXX executable ../bin/demo_dox_sequence_container_view_zip -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_container_view_zip.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o -o ../bin/demo_dox_sequence_container_view_zip -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_sequence_container_view_zip -[ 43%] Linking CXX executable ../bin/demo_dox_graph_algorithms_depth_first_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/link.txt --verbose=1 -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o -o ../bin/demo_dox_graph_algorithms_depth_first_search -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_UNUSED_suffix -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_suffix.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_graph_algorithms_depth_first_search -make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend.internal". -Scanning dependencies of target demo_dox_align_split_split_alignment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build -[ 43%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution2 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution2.dir/link.txt --verbose=1 -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o -o ../bin/demo_tutorial_bed_io_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_bed_io_solution2 -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend.internal". -Scanning dependencies of target demo_tutorial_multiple_sequence_alignment_msa -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > > > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > > > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:57:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1667 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1679 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1701 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::BottomUp<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::BottomUp<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TIndexSpec = void; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 43%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_suffix -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_suffix -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_sequence_UNUSED_suffix -make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_realignment_step1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:44, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h: In instantiation of 'bool seqan::convertAlignment(const seqan::Graph >&, seqan::Align&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TSource = seqan::String, seqan::Alloc<> >; TSpec2 = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:579:21: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:31:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:994:57: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 994 | for(TSize i = 0; i, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -[ 43%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example2 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, FractionalScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FractionalScore = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:482:28: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, TStringSet1&, TNames&, const seqan::MsaOptions&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TStringSet1 = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TNames = seqan::String > >; TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Blosum62_> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:568:23: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, const TScore&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:578:23: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:31:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1667 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1679 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1701 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_sam_and_bam_io_example2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_sam_and_bam_io_example2 -make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/depend +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 14 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, - from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -Scanning dependencies of target demo_dox_index_counting +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/build +[ 41%] Built target demo_tutorial_seed_and_extend_solution6 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/counting.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 43%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_base -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_dox_graph_algorithms_transitive_closure +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/transitive_closure.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:66:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/howto/custom_file_endings.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ @@ -78225,7 +76370,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -78236,25 +76381,25 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ @@ -78264,7 +76409,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ @@ -78272,13 +76417,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ @@ -78286,7 +76431,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 205 | return TProxy(it); | ^~~~~~~~~~ @@ -78296,7 +76441,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' 88 | Proxy(TIterator const _it) | ~~~~~~~~~~~~~~~~^~~ @@ -78304,13 +76449,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 94 | : data_iterator(_other.data_iterator) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ @@ -78319,7 +76464,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -78331,65 +76476,58 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_indexed_fasta_io_base -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:21:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 89 | : data_iterator(_it) | ^ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -78402,22 +76540,16 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target demo_dox_modifier_modified_string_nested -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string_nested.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -78425,38 +76557,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/counting.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 41%] Linking CXX executable ../bin/demo_dox_sequence_string2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_string2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_string2.dir/dox/sequence/string2.cpp.o -o ../bin/demo_dox_sequence_string2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' @@ -78465,29 +76591,36 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_dox_sequence_string2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' @@ -78496,29 +76629,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_tutorial_seed_and_extend_example1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' @@ -78527,26 +76666,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -78557,7 +76696,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ @@ -78575,7 +76714,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' @@ -78584,27 +76723,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:14:42: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' @@ -78616,20 +76755,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' @@ -78641,16 +76780,603 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:16:31: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/dox/store/store_example.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:10:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:10:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 41%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example7 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/tutorial/seed_and_extend/example7.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example7 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_tutorial_seed_and_extend_example7 +make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/depend.internal". +Scanning dependencies of target demo_dox_sequence_segment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 41%] Linking CXX executable ../bin/demo_dox_graph_algorithms_transitive_closure +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/dox/graph_algorithms/transitive_closure.cpp.o -o ../bin/demo_dox_graph_algorithms_transitive_closure -lrt -lz -lbz2 +[ 41%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_index_multiple +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/tutorial/pattern_matching/find_index_multiple.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_index_multiple -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_dox_graph_algorithms_transitive_closure +make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend.internal". +Scanning dependencies of target demo_dox_sequence_container_view_zip +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Building CXX object demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/container_view_zip.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_tutorial_pattern_matching_find_index_multiple +make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_depth_first_search +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/depth_first_search.cpp +[ 43%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_own_function +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/tutorial/parsing_command_line_arguments/example_with_own_function.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_own_function -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_parsing_command_line_arguments_example_with_own_function +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_indexed_fasta_io_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:93:33: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 93 | TExplicitPrefix preB(sufA, 3); + | ^ +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:89:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' + 89 | Segment(typename Parameter_::Type _host, typename Position::Type _end_index): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/example1.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String >; TSpec = seqan::SuffixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:90:29: required from 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:93:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_smart_pointer.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_allocator.h:46, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:74, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h: In instantiation of 'typename seqan::Parameter_::Type seqan::_toParameter(const T&) [with T = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:171:32: required from 'typename seqan::Parameter_::Type seqan::host(const seqan::Segment&) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Parameter_::Type = seqan::Segment >, seqan::SuffixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:206:53: required from 'typename seqan::Iterator, const seqan::Tag >::Type seqan::begin(const seqan::Segment&, Standard) [with THost_ = seqan::Segment >, seqan::SuffixSegment>; typename seqan::Iterator, const seqan::Tag >::Type = char*; seqan::Standard = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1095:69: required from 'typename seqan::EnableIf, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::SuffixSegment>, seqan::PrefixSegment>; typename seqan::EnableIf, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = seqan::Segment >, seqan::SuffixSegment>; TSpec = seqan::PrefixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:94:18: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_type.h:365:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::SuffixSegment>::Segment(const seqan::Segment >, seqan::SuffixSegment>&)' is deprecated [-Wdeprecated-copy] + 365 | return _object; + | ^~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:97, + from /build/seqan2-2.4.0+dfsg/demos/dox/sequence/segment.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_suffix.h:129:5: note: because 'seqan::Segment >, seqan::SuffixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 129 | operator = (Segment const & source) + | ^~~~~~~~ +[ 43%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example7 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/tutorial/sam_and_bam_io/example7.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example7 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_sam_and_bam_io_example7 +make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_segmentalignment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp +[ 43%] Linking CXX executable ../bin/demo_dox_sequence_segment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_segment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_segment.dir/dox/sequence/segment.cpp.o -o ../bin/demo_dox_sequence_segment -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_sequence_segment +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend.internal". +Scanning dependencies of target demo_dox_sequence_UNUSED_suffix +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_suffix.cpp +[ 43%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/tutorial/seed_and_extend/example1.cpp.o -o ../bin/demo_tutorial_seed_and_extend_example1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_seed_and_extend_example1 +make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend.internal". +Scanning dependencies of target demo_dox_align_split_split_alignment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_split/split_alignment.cpp +[ 43%] Linking CXX executable ../bin/demo_howto_efficiently_import_sequences +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_efficiently_import_sequences.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_efficiently_import_sequences.dir/howto/efficiently_import_sequences.cpp.o -o ../bin/demo_howto_efficiently_import_sequences -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_howto_efficiently_import_sequences +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend.internal". +Scanning dependencies of target demo_tutorial_multiple_sequence_alignment_msa +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp +[ 43%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution2.dir/tutorial/bed_io/solution2.cpp.o -o ../bin/demo_tutorial_bed_io_solution2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_bed_io_solution2 +make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend.internal". +[ 43%] Linking CXX executable ../bin/demo_dox_sequence_container_view_zip +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_container_view_zip.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_container_view_zip.dir/dox/sequence/container_view_zip.cpp.o -o ../bin/demo_dox_sequence_container_view_zip -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_realignment_step1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_sequence_container_view_zip +make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/depend.internal". +Scanning dependencies of target demo_dox_index_counting +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/counting.cpp +[ 43%] Linking CXX executable ../bin/demo_dox_graph_algorithms_depth_first_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/dox/graph_algorithms/depth_first_search.cpp.o -o ../bin/demo_dox_graph_algorithms_depth_first_search -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_graph_algorithms_depth_first_search +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend.internal". +Scanning dependencies of target demo_dox_modifier_modified_string_nested +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string_nested.cpp +[ 43%] Linking CXX executable ../bin/demo_howto_custom_file_endings +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_custom_file_endings.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_custom_file_endings.dir/howto/custom_file_endings.cpp.o -o ../bin/demo_howto_custom_file_endings -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_howto_custom_file_endings +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend.internal". +Scanning dependencies of target demo_tutorial_journaled_set_example_online_search +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search.cpp +[ 43%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_suffix +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/dox/sequence/UNUSED_suffix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_suffix -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_sequence_UNUSED_suffix +make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_dox_index_length_countSequences +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:44, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h: In instantiation of 'bool seqan::convertAlignment(const seqan::Graph >&, seqan::Align&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TSource = seqan::String, seqan::Alloc<> >; TSpec2 = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:579:21: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:31:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:994:57: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 994 | for(TSize i = 0; i, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +[ 43%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/tutorial/sam_and_bam_io/example2.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_sam_and_bam_io_example2 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp +[ 43%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/tutorial/journaled_set/solution_online_search_assignment3.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment3 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_journaled_set_solution_online_search_assignment3 +make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, FractionalScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FractionalScore = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:482:28: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, TStringSet1&, TNames&, const seqan::MsaOptions&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TStringSet1 = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TNames = seqan::String > >; TAlphabet = seqan::SimpleType; TScore = seqan::Score, seqan::Blosum62_> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:568:23: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, const TScore&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:578:23: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score, seqan::Blosum62_> >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:31:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1667 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1679 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1701 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/msa.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +Scanning dependencies of target demo_dox_modifier_cyclic_shape +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp +[ 43%] Linking CXX executable ../../bin/test_seeds_align_banded_chain_impl +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_align_banded_chain_impl.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_align_banded_chain_impl.dir/test_align_banded_chain_impl.cpp.o -o ../../bin/test_seeds_align_banded_chain_impl -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/counting.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 43%] Linking CXX executable ../bin/demo_dox_modifier_modified_string_nested +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string_nested.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o -o ../bin/demo_dox_modifier_modified_string_nested -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_modifier_modified_string_nested +make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend.internal". +Scanning dependencies of target demo_dox_misc_interval_tree_example +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -78743,6 +77469,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/dox/index/counting.cpp:3: @@ -78763,70 +77490,389 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 43%] Linking CXX executable ../bin/demo_dox_store_store_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_store_store_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o -o ../bin/demo_dox_store_store_example -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_store_store_example -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_set_example_online_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search.cpp -[ 43%] Linking CXX executable ../bin/demo_dox_modifier_modified_string_nested -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string_nested.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string_nested.dir/dox/modifier/modified_string_nested.cpp.o -o ../bin/demo_dox_modifier_modified_string_nested -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_modifier_modified_string_nested -make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend.internal". -Scanning dependencies of target demo_dox_index_length_countSequences -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp -[ 43%] Linking CXX executable ../bin/demo_dox_align_split_split_alignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_split_split_alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o -o ../bin/demo_dox_align_split_split_alignment -lrt -lz -lbz2 -[ 43%] Linking CXX executable ../bin/demo_dox_index_counting -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_counting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o -o ../bin/demo_dox_index_counting -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_index_counting -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_align_split_split_alignment -make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend +[ 43%] Built target test_seeds_align_banded_chain_impl +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend.internal". -Scanning dependencies of target demo_dox_modifier_cyclic_shape +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp +[ 43%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > > > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > > > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:57:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1667 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1679 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1701 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:40, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::BottomUp<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::BottomUp<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TIndexSpec = void; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:25:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape > >; typename seqan::Size > >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:28:70: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' + 203 | CyclicShape(CyclicShape const & other) : + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:27:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' + 203 | CyclicShape(CyclicShape const & other) : + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > > >; TSource = seqan::Index > > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > > >; TValue2 = seqan::Index > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > > >; typename seqan::Reference > >::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [5]; seqan::FinderMlr = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [5]]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:22:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > > >& seqan::Index > > >::operator=(const seqan::Index > > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' + 429 | Index(Index const &other): + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:48, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:44, @@ -78928,15 +77974,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search.cpp:3: @@ -78965,21 +78002,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape > >; typename seqan::Size > >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:28:70: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' - 203 | CyclicShape(CyclicShape const & other) : - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -79009,23 +78031,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::JournaledStringIterSpec > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:27:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' - 203 | CyclicShape(CyclicShape const & other) : - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -79157,28 +78162,50 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > > >; TSource = seqan::Index > > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > > >; TValue2 = seqan::Index > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > > >; typename seqan::Reference > >::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [5]; seqan::FinderMlr = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [5]]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:22:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > > >& seqan::Index > > >::operator=(const seqan::Index > > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' - 429 | Index(Index const &other): - | ^~~~~ +[ 43%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > >, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = seqan::String >]': +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > >, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = seqan::String >; TValue2 = int]' +/build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:22:42: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1562 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1575 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1598 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters +make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend.internal". +Scanning dependencies of target demo_tutorial_background_and_motivation_example +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/background_and_motivation/example.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:177, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_hirschberg_impl.h: In instantiation of 'TScoreValue seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const Hirschberg&) [with TSequenceH = seqan::String >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; seqan::Hirschberg = seqan::Tag]': @@ -79243,6 +78270,127 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' 105 | Iter(Iter const & other_) : | ^~~~ +[ 43%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/tutorial/indexed_fasta_io/base.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_base -lrt -lz -lbz2 +[ 43%] Linking CXX executable ../bin/demo_dox_modifier_cyclic_shape +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_cyclic_shape.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o -o ../bin/demo_dox_modifier_cyclic_shape -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_indexed_fasta_io_base +make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend.internal". +Scanning dependencies of target demo_tutorial_blast_io_write_assignment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp +[ 43%] Built target demo_dox_modifier_cyclic_shape +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/DependInfo.cmake --color= +[ 43%] Linking CXX executable ../bin/demo_dox_index_counting +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_counting.dir/link.txt --verbose=1 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend.internal". +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_counting.dir/dox/index/counting.cpp.o -o ../bin/demo_dox_index_counting -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_indexed_fasta_io_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution2.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_index_counting +make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:218:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const seqan::StringSet&, TAlgSpec) [with TSA = seqan::String >, seqan::Alloc<> >; TString = seqan::String, seqan::Alloc<> >; TSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:173:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const seqan::StringSet&, const TAlgSpec&, seqan::True) [with TSA = seqan::String >, seqan::Alloc<> >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Owner<>; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +Scanning dependencies of target demo_dox_index_textAt_indexText_saAt_indexRequire +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79269,9 +78417,482 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 43%] Linking CXX executable ../bin/demo_dox_modifier_cyclic_shape -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_cyclic_shape.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_cyclic_shape.dir/dox/modifier/cyclic_shape.cpp.o -o ../bin/demo_dox_modifier_cyclic_shape -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:414:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 5, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:415:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:432:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 4 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:416:33: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::Alloc<> > > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: [ skipping 5 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:24:72: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:161:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:162:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:179:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:190:17: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:173:12: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:367:49: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79382,6 +79003,60 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' @@ -79461,6 +79136,118 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79598,6 +79385,91 @@ | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 9 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' @@ -79650,6 +79522,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79677,7 +79580,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79733,12 +79635,92 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 43%] Built target demo_dox_modifier_cyclic_shape -make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79793,12 +79775,174 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_dox_misc_interval_tree_example +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +[ 43%] Linking CXX executable ../bin/demo_tutorial_background_and_motivation_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_background_and_motivation_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o -o ../bin/demo_tutorial_background_and_motivation_example -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = const char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:16:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 14 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::Alloc<> > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::Alloc<> > > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:37:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:37, + from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/segmentalignment.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:18:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/realignment/step1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp +[ 43%] Built target demo_tutorial_background_and_motivation_example +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79832,6 +79976,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 203 | *I = *refPrev; | ~~~^~~~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -79840,6 +79985,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79854,6 +80000,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_affine_dgs +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_affine_dgs.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/length_countSequences.cpp:1: @@ -79909,101 +80063,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 43%] Linking CXX executable ../bin/demo_tutorial_consensus_alignment_with_positions -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/tutorial/consensus_alignment/with_positions.cpp.o -o ../bin/demo_tutorial_consensus_alignment_with_positions -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_consensus_alignment_with_positions -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > >, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = seqan::String >]': -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > >, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = seqan::String >; TValue2 = int]' -/build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:22:42: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1562 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1575 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>& seqan::IntervalTreeNode > >, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode > >, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1598 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/demos/dox/misc/interval_tree_example.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ [ 43%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/tutorial/pairwise_sequence_alignment/alignment_global_specialised.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 43%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised -make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend.internal". -Scanning dependencies of target demo_tutorial_background_and_motivation_example -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build +make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/background_and_motivation/example.cpp -[ 43%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/unassigned_or_unused/tutorial_sequence/count_generic_characters.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters -lrt -lz -lbz2 -[ 43%] Linking CXX executable ../bin/demo_tutorial_background_and_motivation_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_background_and_motivation_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_background_and_motivation_example.dir/tutorial/background_and_motivation/example.cpp.o -o ../bin/demo_tutorial_background_and_motivation_example -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend.internal". +Scanning dependencies of target demo_dox_parallel_queue_example make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters -make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend +make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend.internal". -Scanning dependencies of target demo_tutorial_blast_io_write_assignment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/parallel/queue_example.cpp +[ 43%] Linking CXX executable ../bin/demo_dox_align_split_split_alignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_split_split_alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_split_split_alignment.dir/dox/align_split/split_alignment.cpp.o -o ../bin/demo_dox_align_split_split_alignment -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_dox_align_split_split_alignment +make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_background_and_motivation_example -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_indexed_fasta_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend.internal". +Scanning dependencies of target demo_tutorial_indices_fm_index make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build +make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution2.cpp -[ 43%] Linking CXX executable ../bin/demo_dox_misc_interval_tree_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_interval_tree_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o -o ../bin/demo_dox_misc_interval_tree_example -lrt -lz -lbz2 +[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/fm_index.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -80030,11 +80121,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_misc_interval_tree_example -make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/DependInfo.cmake --color= +[ 43%] Linking CXX executable ../bin/demo_tutorial_realignment_step2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_realignment_step2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_realignment_step2.dir/tutorial/realignment/step2.cpp.o -o ../bin/demo_tutorial_realignment_step2 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:51:50: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 43%] Linking CXX executable ../../bin/razers3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 && /usr/bin/cmake -E cmake_link_script CMakeFiles/razers3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/razers3.dir/razers.cpp.o CMakeFiles/razers3.dir/param_tabs.cpp.o -o ../../bin/razers3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution2.cpp:3: @@ -80059,26 +80178,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:51:50: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/write_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Built target demo_tutorial_realignment_step2 +make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/depend.internal". +Scanning dependencies of target demo_dox_index_sufarray +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_sufarray.dir/dox/index/sufarray.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_sufarray.dir/dox/index/sufarray.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/sufarray.cpp +[ 43%] Linking CXX executable ../bin/demo_dox_misc_interval_tree_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_interval_tree_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_interval_tree_example.dir/dox/misc/interval_tree_example.cpp.o -o ../bin/demo_dox_misc_interval_tree_example -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution2.cpp:3: @@ -80121,109 +80236,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target demo_dox_index_textAt_indexText_saAt_indexRequire -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 43%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_indexed_fasta_io_solution2 -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_affine_dgs -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_affine_dgs.cpp -[ 43%] Linking CXX executable ../bin/demo_dox_index_textAt_indexText_saAt_indexRequire -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o -o ../bin/demo_dox_index_textAt_indexText_saAt_indexRequire -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_index_textAt_indexText_saAt_indexRequire -make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend.internal". -Scanning dependencies of target demo_dox_parallel_queue_example -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/parallel/queue_example.cpp -[ 43%] Linking CXX executable ../bin/demo_tutorial_realignment_step1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_realignment_step1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o -o ../bin/demo_tutorial_realignment_step1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_realignment_step1 -make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend.internal". -Scanning dependencies of target demo_tutorial_indices_fm_index -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/fm_index.cpp -[ 43%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_online_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o -o ../bin/demo_tutorial_journaled_set_example_online_search -lrt -lz -lbz2 -[ 43%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_msa -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_msa -lrt -lz -lbz2 -[ 43%] Linking CXX executable ../bin/demo_dox_parallel_queue_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_parallel_queue_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o -o ../bin/demo_dox_parallel_queue_example -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_journaled_set_example_online_search -make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_dox_index_sufarray make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/build -[ 43%] Built target demo_dox_parallel_queue_example +[ 43%] Built target demo_dox_misc_interval_tree_example make -f demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph.dir/DependInfo.cmake --color= -[ 43%] Building CXX object demos/CMakeFiles/demo_dox_index_sufarray.dir/dox/index/sufarray.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_sufarray.dir/dox/index/sufarray.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/sufarray.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_tutorial_alignment_graph make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build -[ 43%] Built target demo_tutorial_multiple_sequence_alignment_msa -make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_graph.dir/tutorial/alignment/graph.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_graph.dir/tutorial/alignment/graph.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/graph.cpp +[ 44%] Linking CXX executable ../bin/demo_dox_parallel_queue_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_parallel_queue_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_parallel_queue_example.dir/dox/parallel/queue_example.cpp.o -o ../bin/demo_dox_parallel_queue_example -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 44%] Built target demo_dox_parallel_queue_example +make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_example1.dir/DependInfo.cmake --color= -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_graph.dir/tutorial/alignment/graph.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/graph.cpp Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend.internal". Scanning dependencies of target demo_tutorial_seeds_example1 @@ -80232,20 +80265,8 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object demos/CMakeFiles/demo_tutorial_seeds_example1.dir/tutorial/seeds/example1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seeds_example1.dir/tutorial/seeds/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/example1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/fm_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 44%] Linking CXX executable ../bin/demo_tutorial_blast_io_write_assignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o -o ../bin/demo_tutorial_blast_io_write_assignment -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Built target demo_tutorial_blast_io_write_assignment +[ 44%] Built target razers3 make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/DependInfo.cmake --color= @@ -80257,33 +80278,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/dox/basic/metaprogramming_control.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_control.dir/dox/basic/metaprogramming_control.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_control.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/example1.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 44%] Linking CXX executable ../bin/demo_tutorial_indices_fm_index -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_fm_index.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o -o ../bin/demo_tutorial_indices_fm_index -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/sufarray.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 44%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_control -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_control.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_control.dir/dox/basic/metaprogramming_control.cpp.o -o ../bin/demo_dox_basic_metaprogramming_control -lrt -lz -lbz2 +[ 44%] Linking CXX executable ../bin/demo_dox_index_textAt_indexText_saAt_indexRequire +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/dox/index/textAt_indexText_saAt_indexRequire.cpp.o -o ../bin/demo_dox_index_textAt_indexText_saAt_indexRequire -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Built target demo_tutorial_indices_fm_index +[ 44%] Built target demo_dox_index_textAt_indexText_saAt_indexRequire make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_open_save.dir/DependInfo.cmake --color= @@ -80293,59 +80292,134 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 44%] Building CXX object demos/CMakeFiles/demo_dox_index_open_save.dir/dox/index/open_save.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_open_save.dir/dox/index/open_save.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp -[ 44%] Built target demo_dox_basic_metaprogramming_control +[ 44%] Linking CXX executable ../bin/demo_dox_store_store_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_store_store_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_store_store_example.dir/dox/store/store_example.cpp.o -o ../bin/demo_dox_store_store_example -lrt -lz -lbz2 +[ 44%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_control +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_control.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/fm_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_control.dir/dox/basic/metaprogramming_control.cpp.o -o ../bin/demo_dox_basic_metaprogramming_control -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 44%] Built target demo_dox_store_store_example make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/depend.internal". -[ 44%] Linking CXX executable ../bin/demo_tutorial_seeds_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seeds_example1.dir/link.txt --verbose=1 -Scanning dependencies of target demo_tutorial_pattern_matching_assignment3_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seeds_example1.dir/tutorial/seeds/example1.cpp.o -o ../bin/demo_tutorial_seeds_example1 -lrt -lz -lbz2 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3_solution.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Built target demo_tutorial_seeds_example1 +[ 44%] Built target demo_dox_basic_metaprogramming_control make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_assignment3_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 44%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3_solution.cpp Scanning dependencies of target demo_dox_index_node_predicate make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 45%] Building CXX object demos/CMakeFiles/demo_dox_index_node_predicate.dir/dox/index/node_predicate.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_node_predicate.dir/dox/index/node_predicate.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp -[ 45%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_affine_dgs -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_affine_dgs -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/sufarray.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 45%] Linking CXX executable ../bin/demo_tutorial_indices_fm_index +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_fm_index.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_fm_index.dir/tutorial/indices/fm_index.cpp.o -o ../bin/demo_tutorial_indices_fm_index -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 45%] Built target demo_tutorial_alignment_scoring_scheme_affine_dgs +[ 45%] Built target demo_tutorial_indices_fm_index make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seeds/example1.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ Scanning dependencies of target demo_tutorial_q_gram_index_index_qgram make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 45%] Building CXX object demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/tutorial/q_gram_index/index_qgram.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/tutorial/q_gram_index/index_qgram.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram.cpp -[ 45%] Linking CXX executable ../bin/demo_dox_index_sufarray +[ 45%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_affine_dgs +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/tutorial/alignment/scoring_scheme_affine_dgs.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_affine_dgs -lrt -lz -lbz2 +[ 45%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/tutorial/indexed_fasta_io/solution2.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_solution2 -lrt -lz -lbz2 +[ 45%] Built target demo_tutorial_alignment_scoring_scheme_affine_dgs +make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend.internal". +Scanning dependencies of target demo_dox_modifier_modified_string +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_tutorial_indexed_fasta_io_solution2 +make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/base.cpp +[ 46%] Linking CXX executable ../bin/demo_tutorial_seeds_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seeds_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seeds_example1.dir/tutorial/seeds/example1.cpp.o -o ../bin/demo_tutorial_seeds_example1 -lrt -lz -lbz2 +[ 46%] Linking CXX executable ../bin/demo_dox_index_sufarray cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_sufarray.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_sufarray.dir/dox/index/sufarray.cpp.o -o ../bin/demo_dox_index_sufarray -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 45%] Built target demo_dox_index_sufarray -make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend +[ 46%] Built target demo_tutorial_seeds_example1 +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_dox_index_sufarray +make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -80355,18 +80429,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_assignment_4_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend.internal". -Scanning dependencies of target demo_dox_modifier_modified_string +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_4_solution.cpp +Scanning dependencies of target demo_dox_index_mums make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build +make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string.cpp +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3_solution.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -80375,7 +80453,7 @@ 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -80383,6 +80461,70 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -80404,6 +80546,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::String >; TShapeSpec = seqan::UngappedShape<4>]' 143 | Index(Index const &other): | ^~~~~ +[ 46%] Linking CXX executable ../bin/demo_dox_modifier_modified_string +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o -o ../bin/demo_dox_modifier_modified_string -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 46%] Built target demo_dox_modifier_modified_string +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80428,50 +80595,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80576,26 +80699,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:90:68: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/node_predicate.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80674,6 +80777,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Linking CXX executable ../bin/demo_tutorial_sequences_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o -o ../bin/demo_tutorial_sequences_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80782,6 +80888,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80809,6 +80916,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Built target demo_tutorial_sequences_base +make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alignment_align_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80863,6 +80980,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align_assignment1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -80945,15 +81064,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/q_gram_index/index_qgram.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 46%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment3_solution -lrt -lz -lbz2 +[ 46%] Linking CXX executable ../bin/demo_tutorial_alignment_graph +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_graph.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -81008,6 +81123,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_graph.dir/tutorial/alignment/graph.cpp.o -o ../bin/demo_tutorial_alignment_graph -lrt -lz -lbz2 +[ 46%] Linking CXX executable ../bin/demo_tutorial_blast_io_write_assignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/link.txt --verbose=1 +[ 46%] Linking CXX executable ../bin/demo_dox_index_node_predicate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_node_predicate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/tutorial/blast_io/write_assignment.cpp.o -o ../bin/demo_tutorial_blast_io_write_assignment -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_node_predicate.dir/dox/index/node_predicate.cpp.o -o ../bin/demo_dox_index_node_predicate -lrt -lz -lbz2 +[ 46%] Built target demo_tutorial_pattern_matching_assignment3_solution +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_tutorial_alignment_graph +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend.internal". +Scanning dependencies of target demo_dox_modifier_modified_string_mod_view +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string_mod_view.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_seed_and_extend_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -81063,6 +81209,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_dox_index_node_predicate +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake --color= +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution3.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/base.cpp +[ 46%] Built target demo_tutorial_blast_io_write_assignment +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/open_save.cpp:1: @@ -81118,111 +81286,53 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 46%] Linking CXX executable ../bin/demo_dox_index_length_countSequences -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_length_countSequences.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o -o ../bin/demo_dox_index_length_countSequences -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_index_length_countSequences -make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_base +Scanning dependencies of target demo_dox_sequence_UNUSED_infix make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/build +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/base.cpp +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_infix.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ [ 46%] Linking CXX executable ../bin/demo_tutorial_q_gram_index_index_qgram cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/tutorial/q_gram_index/index_qgram.cpp.o -o ../bin/demo_tutorial_q_gram_index_index_qgram -lrt -lz -lbz2 -[ 46%] Linking CXX executable ../bin/demo_dox_modifier_modified_string -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string.dir/dox/modifier/modified_string.cpp.o -o ../bin/demo_dox_modifier_modified_string -lrt -lz -lbz2 +[ 46%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_4_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_4_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 46%] Built target demo_tutorial_q_gram_index_index_qgram -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend.internal". -[ 46%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment3_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/tutorial/pattern_matching/assignment3_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment3_solution -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_sequences_assignment_4_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_4_solution.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_modifier_modified_string -make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/depend.internal". -Scanning dependencies of target demo_dox_index_mums -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_tutorial_pattern_matching_assignment3_solution -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake --color= -[ 46%] Linking CXX executable ../bin/demo_dox_index_node_predicate -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_node_predicate.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_node_predicate.dir/dox/index/node_predicate.cpp.o -o ../bin/demo_dox_index_node_predicate -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_simple_rna_seq_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_index_node_predicate -make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alignment_align_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution4 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align_assignment1.cpp -[ 46%] Linking CXX executable ../bin/demo_tutorial_alignment_graph -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_graph.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_graph.dir/tutorial/alignment/graph.cpp.o -o ../bin/demo_tutorial_alignment_graph -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_tutorial_alignment_graph -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend +[ 46%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution4.cpp +[ 46%] Built target demo_tutorial_sequences_assignment_4_solution +make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend.internal". +Scanning dependencies of target demo_dox_index_maxrepeats make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build +make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution3.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/maxrepeats.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -81303,122 +81413,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 46%] Linking CXX executable ../bin/demo_tutorial_sequences_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_base.dir/tutorial/sequences/base.cpp.o -o ../bin/demo_tutorial_sequences_base -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_tutorial_sequences_base -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend.internal". -Scanning dependencies of target demo_dox_modifier_modified_string_mod_view -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/modified_string_mod_view.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 46%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_4_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/tutorial/sequences/assignment_4_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_4_solution -lrt -lz -lbz2 +[ 46%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_online_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/tutorial/journaled_set/example_online_search.cpp.o -o ../bin/demo_tutorial_journaled_set_example_online_search -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_tutorial_sequences_assignment_4_solution -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend +[ 46%] Built target demo_tutorial_journaled_set_example_online_search +make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend.internal". +Scanning dependencies of target demo_dox_consensus_consensus_alignment make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build +make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/base.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution3.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -81635,6 +81645,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Linking CXX executable ../bin/demo_dox_modifier_modified_string_mod_view +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o -o ../bin/demo_dox_modifier_modified_string_mod_view -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -81770,6 +81783,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_infix +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_infix -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_dox_modifier_modified_string_mod_view +make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -81824,6 +81847,23 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target demo_blast_blast_in_lowlevel +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_dox_sequence_UNUSED_infix +[ 46%] Building CXX object demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o +make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/blast/blast_in_lowlevel.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend.internal". +Scanning dependencies of target demo_dox_bed_io_UNUSED_bed_stream_read +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -81851,6 +81891,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 46%] Building CXX object demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bed_io/UNUSED_bed_stream_read.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -81960,9 +82002,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 46%] Linking CXX executable ../bin/demo_tutorial_alignment_align_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o -o ../bin/demo_tutorial_alignment_align_assignment1 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -82018,6 +82084,37 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 47%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution4 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mums.cpp:3: @@ -82073,73 +82170,48 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_tutorial_alignment_align_assignment1 -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_UNUSED_infix -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_infix.cpp -[ 46%] Linking CXX executable ../bin/demo_dox_modifier_modified_string_mod_view -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/dox/modifier/modified_string_mod_view.cpp.o -o ../bin/demo_dox_modifier_modified_string_mod_view -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_modifier_modified_string_mod_view -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_solution4 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/solution4.cpp -[ 46%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_infix -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/dox/sequence/UNUSED_infix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_infix -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_sequence_UNUSED_infix -make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend.internal". -Scanning dependencies of target demo_dox_index_maxrepeats -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Building CXX object demos/CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/maxrepeats.cpp -[ 47%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/unassigned_or_unused/tutorials_custim_io/solution4.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_solution4 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/base.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 47%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution4 -make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend +make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend.internal". -Scanning dependencies of target demo_dox_consensus_consensus_alignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend.internal". +Scanning dependencies of target demo_dox_index_supermaxrepeats make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build +make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp -[ 47%] Linking CXX executable ../../bin/test_sequence_v2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence_v2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o -o ../../bin/test_sequence_v2 -lrt -lz -lbz2 -[ 47%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_base -lrt -lz -lbz2 +[ 47%] Building CXX object demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution3.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/index/maxrepeats.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -82149,24 +82221,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 47%] Linking CXX executable ../bin/demo_tutorial_alignment_align_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/tutorial/alignment/align_assignment1.cpp.o -o ../bin/demo_tutorial_alignment_align_assignment1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_tutorial_simple_rna_seq_base -make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend +[ 47%] Built target demo_tutorial_alignment_align_assignment1 +make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend.internal". -Scanning dependencies of target demo_blast_blast_in_lowlevel +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/depend.internal". +Scanning dependencies of target demo_howto_scores_load_score make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build +make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/blast/blast_in_lowlevel.cpp -[ 47%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution3 -lrt -lz -lbz2 -[ 47%] Linking CXX executable ../bin/demo_unassigned_or_unused_segmentalignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/link.txt --verbose=1 +[ 47%] Building CXX object demos/CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/scores/load_score.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -82185,12 +82255,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o -o ../bin/demo_unassigned_or_unused_segmentalignment -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_tutorial_seed_and_extend_solution3 -make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/dox/index/maxrepeats.cpp:4: @@ -82217,8 +82281,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/dox/index/maxrepeats.cpp:4: @@ -82239,25 +82301,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -Scanning dependencies of target demo_dox_bed_io_UNUSED_bed_stream_read -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bed_io/UNUSED_bed_stream_read.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_unassigned_or_unused_segmentalignment -make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend.internal". -Scanning dependencies of target demo_dox_index_supermaxrepeats -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/dox/bed_io/UNUSED_bed_stream_read.cpp:2: @@ -82306,9 +82349,18 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 47%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_base -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 47%] Linking CXX executable ../bin/demo_tutorial_realignment_step1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_realignment_step1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_realignment_step1.dir/tutorial/realignment/step1.cpp.o -o ../bin/demo_tutorial_realignment_step1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -82320,35 +82372,153 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 47%] Linking CXX executable ../../bin/test_seeds_banded_chain_alignment_interface -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/test_banded_chain_alignment_interface.cpp.o -o ../../bin/test_seeds_banded_chain_alignment_interface -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_tutorial_parsing_command_line_arguments_base -make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/depend.internal". -Scanning dependencies of target demo_howto_scores_load_score -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/scores/load_score.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::BottomUp<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::BottomUp<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs.h:121:33: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index > >; seqan::Iter > >::TSize = unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:19:74: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 47%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/tutorial/simple_rna_seq/base.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_base -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target test_sequence_v2 +[ 47%] Built target demo_tutorial_realignment_step1 make -f demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build.make demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/depend.internal". +[ 47%] Built target demo_tutorial_simple_rna_seq_base +make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend.internal". Scanning dependencies of target demo_dox_basic_zip_iterator make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build.make demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 47%] Building CXX object demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/dox/basic/zip_iterator.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_zip_iterator.dir/dox/basic/zip_iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/zip_iterator.cpp +Scanning dependencies of target demo_dox_graph_algorithms_bellman_ford_algorithm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/bellman_ford_algorithm.cpp +[ 47%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_msa +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/tutorial/multiple_sequence_alignment/msa.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_msa -lrt -lz -lbz2 +[ 47%] Linking CXX executable ../bin/demo_blast_blast_in_lowlevel +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_blast_blast_in_lowlevel.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o -o ../bin/demo_blast_blast_in_lowlevel -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_tutorial_multiple_sequence_alignment_msa +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_blast_blast_in_lowlevel +make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/DependInfo.cmake --color= +Scanning dependencies of target demo_tutorial_seed_and_extend_solution5 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend.internal". +[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution5.cpp +Scanning dependencies of target demo_tutorial_bed_io_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/base.cpp +[ 47%] Linking CXX executable ../bin/demo_tutorial_consensus_alignment_with_positions +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/tutorial/consensus_alignment/with_positions.cpp.o -o ../bin/demo_tutorial_consensus_alignment_with_positions -lrt -lz -lbz2 +[ 47%] Linking CXX executable ../bin/demo_dox_index_maxrepeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_maxrepeats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o -o ../bin/demo_dox_index_maxrepeats -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -82368,6 +82538,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_dox_index_maxrepeats +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_dox_basic_metaprogramming_logic +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_tutorial_consensus_alignment_with_positions +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, @@ -82398,6 +82584,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 47%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_logic.cpp +Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_matrix +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_matrix.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -82467,15 +82663,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 47%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/tutorial/parsing_command_line_arguments/base.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_base -lrt -lz -lbz2 +[ 47%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/tutorial/seed_and_extend/solution3.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:42, @@ -82507,6 +82700,18 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_tutorial_parsing_command_line_arguments_base +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend.internal". +[ 47%] Built target demo_tutorial_seed_and_extend_solution3 +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -82547,43 +82752,42 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_iterators_assignment_2_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 48%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/tutorial/iterators/assignment_2_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/tutorial/iterators/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_2_solution.cpp +Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 49%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution2.cpp +[ 49%] Linking CXX executable ../bin/demo_dox_index_length_countSequences +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_length_countSequences.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_length_countSequences.dir/dox/index/length_countSequences.cpp.o -o ../bin/demo_dox_index_length_countSequences -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h: In instantiation of 'void seqan::AnsonMyersRealignmentRound_::_subtractReadAlignment(unsigned int, unsigned int&, seqan::AnsonMyersRealignmentRound_::TProfileString&, seqan::ExtractProfileInfo_&, seqan::AnsonMyersRealignmentRound_::TAlignedReadElement, int, const seqan::WindowClippingInfo_&) [with TFragmentStore = seqan::FragmentStore<>; seqan::AnsonMyersRealignmentRound_::TProfileString = seqan::String >, seqan::Alloc<> >; seqan::AnsonMyersRealignmentRound_::TAlignedReadElement = seqan::AlignedReadStoreElement, void>]': /build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1138:9: required from 'void seqan::AnsonMyersRealignmentRound_::run(unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:46:38: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, - from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:685:18: required from 'void seqan::AnsonMyersRealigner_::run(unsigned int, unsigned int, unsigned int&) [with TFragmentStore = seqan::FragmentStore<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:1801:18: required from 'void seqan::reAlignment(seqan::FragmentStore&, unsigned int, unsigned int, unsigned int, bool, unsigned int, unsigned int, bool, bool) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:145:24: required from 'void seqan::consensusAlignment(seqan::FragmentStore&, const seqan::ConsensusAlignmentOptions&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:46:38: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/realign/realign_base.h:404:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 404 | for (TReadGapsIter itR2 = itR; itR2 != itREnd; ++itR2) + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, + from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -82609,68 +82813,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::BottomUp<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::BottomUp<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs.h:121:33: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index > >; seqan::Iter > >::TSize = unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:19:74: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:34:63: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/supermaxrepeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 49%] Built target demo_dox_index_length_countSequences +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:223, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -82692,6 +82845,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +[ 49%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp +[ 49%] Linking CXX executable ../bin/demo_dox_bed_io_UNUSED_bed_stream_read +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o -o ../bin/demo_dox_bed_io_UNUSED_bed_stream_read -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 49%] Built target demo_dox_bed_io_UNUSED_bed_stream_read +make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_align_graph_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_align/graph_align.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -82768,9 +82939,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 47%] Linking CXX executable ../bin/demo_dox_index_maxrepeats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_maxrepeats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_maxrepeats.dir/dox/index/maxrepeats.cpp.o -o ../bin/demo_dox_index_maxrepeats -lrt -lz -lbz2 +[ 50%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_logic +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o -o ../bin/demo_dox_basic_metaprogramming_logic -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -82859,10 +83030,28 @@ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_dox_index_maxrepeats -make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend +[ 50%] Linking CXX executable ../bin/demo_dox_index_supermaxrepeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_supermaxrepeats.dir/link.txt --verbose=1 +[ 50%] Built target demo_dox_basic_metaprogramming_logic +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o -o ../bin/demo_dox_index_supermaxrepeats -lrt -lz -lbz2 +make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend.internal". +Scanning dependencies of target demo_tutorial_generic_programming_example_hashing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/generic_programming/example_hashing.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_index_supermaxrepeats +make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -82898,6 +83087,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +Scanning dependencies of target demo_dox_parallel_splitter_example In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, @@ -82924,6 +83114,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -82958,8 +83150,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend.internal". +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, TIntegral) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; TIntegral = unsigned int]': /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:910:48: required from 'bool seqan::_nextNonRepeatRange(TFinder&, seqan::Pattern >&) [with TFinder = seqan::Finder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Pigeonhole<> >; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/index/find_pigeonhole.h:1006:37: required from 'bool seqan::find(seqan::Finder >&, seqan::Pattern >&, double) [with THaystack = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIndex = seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >; TSpec = void]' @@ -82989,10 +83180,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -Scanning dependencies of target demo_dox_graph_algorithms_bellman_ford_algorithm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/parallel/splitter_example.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -83014,7 +83203,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -[ 47%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -83027,7 +83215,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/bellman_ford_algorithm.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -83040,9 +83227,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -[ 47%] Linking CXX executable ../bin/demo_blast_blast_in_lowlevel -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_blast_blast_in_lowlevel.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_blast_blast_in_lowlevel.dir/blast/blast_in_lowlevel.cpp.o -o ../bin/demo_blast_blast_in_lowlevel -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -83164,11 +83348,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_blast_blast_in_lowlevel -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -83223,14 +83402,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_solution5 +[ 50%] Linking CXX executable ../bin/demo_tutorial_bed_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o -o ../bin/demo_tutorial_bed_io_base -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build +[ 50%] Built target demo_tutorial_bed_io_base +make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution5.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -83260,6 +83441,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 50%] Linking CXX executable ../bin/demo_dox_basic_zip_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_zip_iterator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_zip_iterator.dir/dox/basic/zip_iterator.cpp.o -o ../bin/demo_dox_basic_zip_iterator -lrt -lz -lbz2 +Scanning dependencies of target demo_dox_index_getOccurrences_getFrequency_range_getFibre +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -83325,6 +83515,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_basic_zip_iterator +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:47, from /build/seqan2-2.4.0+dfsg/demos/dox/consensus/consensus_alignment.cpp:3: @@ -83351,6 +83548,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_a_first_example_example_tempSubclassing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/example_tempSubclassing.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:40, @@ -83523,6 +83726,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 50%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tempSubclassing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o -o ../bin/demo_tutorial_a_first_example_example_tempSubclassing -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -83561,6 +83767,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_tutorial_a_first_example_example_tempSubclassing +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -83599,6 +83812,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +Scanning dependencies of target demo_dox_index_begin_atEnd_representative +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative.cpp +[ 50%] Linking CXX executable ../bin/demo_dox_graph_algorithms_bellman_ford_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_bellman_ford_algorithm -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_graph_algorithms_bellman_ford_algorithm +make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_bed_io_example1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp +[ 50%] Linking CXX executable ../bin/demo_tutorial_generic_programming_example_hashing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o -o ../bin/demo_tutorial_generic_programming_example_hashing -lrt -lz -lbz2 /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' @@ -83632,67 +83870,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 47%] Linking CXX executable ../bin/demo_dox_basic_zip_iterator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_zip_iterator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_zip_iterator.dir/dox/basic/zip_iterator.cpp.o -o ../bin/demo_dox_basic_zip_iterator -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target test_seeds_banded_chain_alignment_interface -make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_bed_io_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/base.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_dox_basic_zip_iterator -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend.internal". -[ 47%] Linking CXX executable ../bin/demo_dox_bed_io_UNUSED_bed_stream_read -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/link.txt --verbose=1 -Scanning dependencies of target demo_dox_basic_metaprogramming_logic -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_logic.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/dox/bed_io/UNUSED_bed_stream_read.cpp.o -o ../bin/demo_dox_bed_io_UNUSED_bed_stream_read -lrt -lz -lbz2 -[ 47%] Linking CXX executable ../bin/demo_dox_index_supermaxrepeats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_supermaxrepeats.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_dox_bed_io_UNUSED_bed_stream_read -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_supermaxrepeats.dir/dox/index/supermaxrepeats.cpp.o -o ../bin/demo_dox_index_supermaxrepeats -lrt -lz -lbz2 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alignment_scoring_scheme_matrix -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/scoring_scheme_matrix.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_dox_index_supermaxrepeats -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend +[ 50%] Built target demo_tutorial_generic_programming_example_hashing +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_iterators_assignment_2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend.internal". +[ 50%] Linking CXX executable ../bin/demo_howto_scores_load_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_scores_load_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o -o ../bin/demo_howto_scores_load_score -lrt -lz -lbz2 +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 48%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/tutorial/iterators/assignment_2_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/tutorial/iterators/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_2_solution.cpp +[ 50%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution5.cpp:3: @@ -83703,116 +83896,51 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 48%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_logic -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/dox/basic/metaprogramming_logic.cpp.o -o ../bin/demo_dox_basic_metaprogramming_logic -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 48%] Linking CXX executable ../bin/demo_dox_graph_algorithms_bellman_ford_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/link.txt --verbose=1 -[ 48%] Built target demo_dox_basic_metaprogramming_logic -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/dox/graph_algorithms/bellman_ford_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_bellman_ford_algorithm -lrt -lz -lbz2 -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 49%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution2.cpp -[ 49%] Built target demo_dox_graph_algorithms_bellman_ford_algorithm -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake --color= -[ 49%] Linking CXX executable ../bin/demo_tutorial_bed_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_base.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_base.dir/tutorial/bed_io/base.cpp.o -o ../bin/demo_tutorial_bed_io_base -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 49%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 49%] Built target demo_tutorial_bed_io_base -make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_align_graph_align -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Building CXX object demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_align/graph_align.cpp -[ 50%] Linking CXX executable ../bin/demo_howto_scores_load_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_scores_load_score.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_scores_load_score.dir/howto/scores/load_score.cpp.o -o ../bin/demo_howto_scores_load_score -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_howto_scores_load_score -make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend.internal". -Scanning dependencies of target demo_tutorial_generic_programming_example_hashing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/generic_programming/example_hashing.cpp [ 50%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_2_solution cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/tutorial/iterators/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_2_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/link.txt --verbose=1 -[ 50%] Built target demo_tutorial_iterators_assignment_2_solution -make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend +[ 50%] Built target demo_howto_scores_load_score +make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution5 -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend.internal". -[ 50%] Linking CXX executable ../bin/demo_tutorial_generic_programming_example_hashing -Scanning dependencies of target demo_dox_parallel_splitter_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend.internal". +Scanning dependencies of target demo_dox_basic_enable_if make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/link.txt --verbose=1 +make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/tutorial/generic_programming/example_hashing.cpp.o -o ../bin/demo_tutorial_generic_programming_example_hashing -lrt -lz -lbz2 -[ 50%] Building CXX object demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/parallel/splitter_example.cpp +[ 50%] Building CXX object demos/CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/enable_if.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_tutorial_seed_and_extend_solution5 -make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend +[ 50%] Built target demo_tutorial_iterators_assignment_2_solution +make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend.internal". +[ 50%] Linking CXX executable ../bin/demo_dox_parallel_splitter_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_parallel_splitter_example.dir/link.txt --verbose=1 +Scanning dependencies of target demo_dox_sequence_stringset make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_tutorial_generic_programming_example_hashing -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend +make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_example_tempSubclassing +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o -o ../bin/demo_dox_parallel_splitter_example -lrt -lz -lbz2 +[ 51%] Building CXX object demos/CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/stringset.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build +[ 51%] Built target demo_dox_parallel_splitter_example +make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_dox_index_getOccurrences_getFrequency_range_getFibre +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend.internal". +Scanning dependencies of target demo_dox_align_global_alignment_unbanded make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build -[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/example_tempSubclassing.cpp +make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 51%] Building CXX object demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_unbanded.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution2.cpp:1: @@ -83838,9 +83966,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 50%] Building CXX object demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp -[ 50%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tempSubclassing +[ 51%] Linking CXX executable ../bin/demo_dox_basic_enable_if +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_enable_if.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o -o ../bin/demo_dox_basic_enable_if -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution2.cpp:1: @@ -83867,8 +83995,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/tutorial/a_first_example/example_tempSubclassing.cpp.o -o ../bin/demo_tutorial_a_first_example_example_tempSubclassing -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 51%] Built target demo_dox_basic_enable_if +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, @@ -83890,54 +84023,92 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_unassigned_or_unused_benchmark_stream make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_tutorial_a_first_example_example_tempSubclassing -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend.internal". -Scanning dependencies of target demo_dox_index_begin_atEnd_representative -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative.cpp -[ 50%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step1 +[ 51%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:7:84: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 51%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/tutorial/pairwise_sequence_alignment/assignment5_step1.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step1 -lrt -lz -lbz2 -[ 50%] Linking CXX executable ../bin/demo_dox_parallel_splitter_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_parallel_splitter_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_parallel_splitter_example.dir/dox/parallel/splitter_example.cpp.o -o ../bin/demo_dox_parallel_splitter_example -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_dox_parallel_splitter_example +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:7:84: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 51%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend -[ 50%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/tutorial/seed_and_extend/solution5.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution5 -lrt -lz -lbz2 +[ 51%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend.internal". -Scanning dependencies of target demo_tutorial_bed_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend.internal". +Scanning dependencies of target demo_dox_index_begin_atEnd_representative_bottomUp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn +[ 51%] Built target demo_tutorial_seed_and_extend_solution5 +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake --color= +[ 52%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/dox/index/begin_atEnd_representative_bottomUp.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/dox/index/begin_atEnd_representative_bottomUp.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative_bottomUp.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_find_index make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp -[ 50%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp -[ 50%] Linking CXX executable ../bin/demo_dox_index_open_save -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_open_save.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_open_save.dir/dox/index/open_save.cpp.o -o ../bin/demo_dox_index_open_save -lrt -lz -lbz2 +[ 52%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -84016,6 +84187,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +[ 52%] Linking CXX executable ../bin/demo_dox_sequence_stringset +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_stringset.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o -o ../bin/demo_dox_sequence_stringset -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TSpec2 = seqan::ParentLinks<>; TIndex = seqan::Index > >; TSpec = seqan::Preorder]': @@ -84108,6 +84282,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 52%] Built target demo_dox_sequence_stringset +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend.internal". +Scanning dependencies of target demo_dox_basic_metaprogramming_math +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': @@ -84124,6 +84309,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +[ 52%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_math.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative.cpp:1: @@ -84219,86 +84406,51 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 50%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_matrix -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_matrix -lrt -lz -lbz2 +[ 53%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 50%] Built target demo_dox_index_open_save -make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend +[ 53%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn +make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:7:84: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_dox_basic_enable_if +make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 53%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp +[ 53%] Linking CXX executable ../bin/demo_tutorial_alignment_scoring_scheme_matrix +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/tutorial/alignment/scoring_scheme_matrix.cpp.o -o ../bin/demo_tutorial_alignment_scoring_scheme_matrix -lrt -lz -lbz2 +[ 53%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_math +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_math.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o -o ../bin/demo_dox_basic_metaprogramming_math -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/build -[ 50%] Built target demo_tutorial_alignment_scoring_scheme_matrix -make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend +[ 53%] Built target demo_tutorial_alignment_scoring_scheme_matrix +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 53%] Built target demo_dox_basic_metaprogramming_math +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/DependInfo.cmake --color= -[ 50%] Building CXX object demos/CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/enable_if.cpp -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:7:84: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target demo_dox_sequence_stringset +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend.internal". +Scanning dependencies of target demo_tutorial_fragment_store_access_aligned_reads2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/build +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 51%] Building CXX object demos/CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/stringset.cpp -[ 51%] Linking CXX executable ../bin/demo_dox_basic_enable_if -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_enable_if.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_enable_if.dir/dox/basic/enable_if.cpp.o -o ../bin/demo_dox_basic_enable_if -lrt -lz -lbz2 +[ 54%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads2.cpp +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_local +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: @@ -84325,7 +84477,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 55%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: @@ -84434,12 +84588,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 51%] Built target demo_dox_basic_enable_if -make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: @@ -84521,12 +84669,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_dox_align_global_alignment_unbanded -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 51%] Building CXX object demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_unbanded.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: @@ -84907,6 +85049,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative_bottomUp.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp:1: @@ -84962,111 +85122,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 52%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/unassigned_or_unused/tutorials_custim_io/parse_blastn.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn -lrt -lz -lbz2 -[ 52%] Linking CXX executable ../bin/demo_dox_index_begin_atEnd_representative -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o -o ../bin/demo_dox_index_begin_atEnd_representative -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 52%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 52%] Built target demo_dox_index_begin_atEnd_representative -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_benchmark_stream -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_dox_index_begin_atEnd_representative_bottomUp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build -[ 52%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp -[ 53%] Building CXX object demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/dox/index/begin_atEnd_representative_bottomUp.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/dox/index/begin_atEnd_representative_bottomUp.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative_bottomUp.cpp -[ 53%] Linking CXX executable ../bin/demo_dox_graph_align_graph_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_align_graph_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o -o ../bin/demo_dox_graph_align_graph_align -lrt -lz -lbz2 -[ 53%] Linking CXX executable ../bin/demo_dox_sequence_stringset -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_stringset.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_stringset.dir/dox/sequence/stringset.cpp.o -o ../bin/demo_dox_sequence_stringset -lrt -lz -lbz2 -[ 53%] Built target demo_dox_graph_align_graph_align -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake --color= -[ 53%] Linking CXX executable ../bin/demo_dox_index_mums -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_mums.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o -o ../bin/demo_dox_index_mums -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_pattern_matching_find_index -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Built target demo_dox_sequence_stringset -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend.internal". -Scanning dependencies of target demo_dox_basic_metaprogramming_math -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_math.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Built target demo_dox_index_mums -make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp -[ 53%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_math -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_math.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_math.dir/dox/basic/metaprogramming_math.cpp.o -o ../bin/demo_dox_basic_metaprogramming_math -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 53%] Built target demo_dox_basic_metaprogramming_math -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_fragment_store_access_aligned_reads2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 54%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads2.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative_bottomUp.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/dox/index/begin_atEnd_representative_bottomUp.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Postorder]': @@ -85159,96 +85214,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:95:28: required from 'int seqan::globalAlignment(seqan::Align&, const MyersHirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:22:52: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 348 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 368 | finger2 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 370 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 398 | finger1 = begin(matrix_); - | ~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 423 | it_ = finger1; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -[ 54%] Linking CXX executable ../bin/demo_tutorial_bed_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_example1.dir/link.txt --verbose=1 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o -o ../bin/demo_tutorial_bed_io_example1 -lrt -lz -lbz2 -[ 54%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution2 -lrt -lz -lbz2 +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > >; TSource = seqan::Index > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > >; TValue2 = seqan::Index > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > >; typename seqan::Reference > >::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:569:26: required from 'typename seqan::InfixOnValue::Type seqan::infix(seqan::Finder&) [with THaystack = seqan::Index > >; TSpec = const seqan::Tag; typename seqan::InfixOnValue::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:18:105: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > >& seqan::Index > >::operator=(const seqan::Index > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' + 429 | Index(Index const &other): + | ^~~~~ +[ 55%] Linking CXX executable ../bin/demo_dox_index_begin_atEnd_representative +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/dox/index/begin_atEnd_representative.cpp.o -o ../bin/demo_dox_index_begin_atEnd_representative -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 54%] Built target demo_tutorial_bed_io_example1 -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend +[ 55%] Built target demo_dox_index_begin_atEnd_representative +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_assignment_2_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 55%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_2_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -85273,25 +85275,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_local -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build -[ 54%] Built target demo_tutorial_sam_and_bam_io_solution2 -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake --color= -[ 55%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend.internal". -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp -Scanning dependencies of target demo_tutorial_sequences_assignment_2_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 55%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_2_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': @@ -85316,6 +85299,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 55%] Linking CXX executable ../bin/demo_tutorial_bed_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_example1.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -85341,27 +85326,88 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_example1.dir/tutorial/bed_io/example1.cpp.o -o ../bin/demo_tutorial_bed_io_example1 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_specialized.h:95:28: required from 'int seqan::globalAlignment(seqan::Align&, const MyersHirschberg&) [with TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:22:52: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:348:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 348 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index > >; TSource = seqan::Index > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index > >; TValue2 = seqan::Index > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index > >; typename seqan::Reference > >::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder > > >; typename seqan::Parameter_::Type>::Type = seqan::Index > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:569:26: required from 'typename seqan::InfixOnValue::Type seqan::infix(seqan::Finder&) [with THaystack = seqan::Index > >; TSpec = const seqan::Tag; typename seqan::InfixOnValue::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:18:105: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index > >& seqan::Index > >::operator=(const seqan::Index > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_index.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' - 429 | Index(Index const &other): - | ^~~~~ + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:368:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 368 | finger2 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:370:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 370 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:398:21: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 398 | finger1 = begin(matrix_); + | ~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h:423:25: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 423 | it_ = finger1; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 55%] Built target demo_tutorial_bed_io_example1 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_all_pairs_shortest_path +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 55%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/all_pairs_shortest_path.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': @@ -85433,6 +85479,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 55%] Linking CXX executable ../bin/demo_dox_align_global_alignment_unbanded +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o -o ../bin/demo_dox_align_global_alignment_unbanded -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': @@ -85458,6 +85507,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 55%] Built target demo_dox_align_global_alignment_unbanded +make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/benchmark_stream.cpp:51: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': @@ -85483,25 +85539,302 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 55%] Linking CXX executable ../bin/demo_dox_index_begin_atEnd_representative_bottomUp +Scanning dependencies of target demo_dox_bam_io_bam_tags_dict +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 56%] Building CXX object demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_tags_dict.cpp +[ 56%] Linking CXX executable ../bin/demo_dox_graph_align_graph_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_align_graph_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_align_graph_align.dir/dox/graph_align/graph_align.cpp.o -o ../bin/demo_dox_graph_align_graph_align -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 56%] Built target demo_dox_graph_align_graph_align +make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_longest_common_subsequence +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 58%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/longest_common_subsequence.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 235 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 253 | finger2 = col_; //points to last column + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 255 | finger1 = col_; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 595 | it_ = source_; + | ~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 445 | finger1 = end_col; //points to last column + | ~~~~~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 447 | finger0 = end_col; + | ~~~~~~~~^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 647 | return Iter >(container(left), hostIterator(left) - right); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 486 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 58%] Linking CXX executable ../bin/demo_dox_index_begin_atEnd_representative_bottomUp cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/dox/index/begin_atEnd_representative_bottomUp.cpp.o -o ../bin/demo_dox_index_begin_atEnd_representative_bottomUp -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 55%] Built target demo_dox_index_begin_atEnd_representative_bottomUp -make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend +[ 58%] Built target demo_dox_index_begin_atEnd_representative_bottomUp +make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake --color= -[ 55%] Linking CXX executable ../bin/demo_dox_align_global_alignment_unbanded -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/dox/align/global_alignment_unbanded.cpp.o -o ../bin/demo_dox_align_global_alignment_unbanded -lrt -lz -lbz2 -Scanning dependencies of target demo_dox_graph_algorithms_all_pairs_shortest_path +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/depend.internal". +Scanning dependencies of target demo_dox_index_finder make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build +make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 55%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/all_pairs_shortest_path.cpp +[ 58%] Building CXX object demos/CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/finder.cpp +[ 58%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_index +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_index -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 58%] Built target demo_tutorial_pattern_matching_find_index +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_file_speed +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 58%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_speed.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85529,17 +85862,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 55%] Built target demo_dox_align_global_alignment_unbanded -make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend.internal". -Scanning dependencies of target demo_dox_bam_io_bam_tags_dict -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 58%] Linking CXX executable ../bin/demo_tutorial_a_first_example_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o -o ../bin/demo_tutorial_a_first_example_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85568,10 +85893,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 56%] Building CXX object demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_tags_dict.cpp -[ 56%] Linking CXX executable ../bin/demo_tutorial_a_first_example_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_base.dir/link.txt --verbose=1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 58%] Built target demo_tutorial_a_first_example_base +make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/depend.internal". +Scanning dependencies of target demo_dox_find_finder_online +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_online.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads2.cpp:3: @@ -85591,7 +85925,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_base.dir/tutorial/a_first_example/base.cpp.o -o ../bin/demo_tutorial_a_first_example_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85622,13 +85955,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 56%] Built target demo_tutorial_a_first_example_base -make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85691,12 +86017,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_dox_graph_algorithms_longest_common_subsequence -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/longest_common_subsequence.cpp +[ 59%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_2_solution -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85754,6 +86077,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Built target demo_tutorial_sequences_assignment_2_solution +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_interval_tree In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -85785,6 +86116,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/interval_tree.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -85835,280 +86171,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:16: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 714 | best_begin = _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,(top(sw_finder.pQ)).id_), score_); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:748:20: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 748 | next_best_begin= _smithWatermanTrace(gapsH, gapsV, sw_finder.forbidden,iter(sw_finder.matrix,next_best_end), score_); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:235:13: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 235 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:253:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 253 | finger2 = col_; //points to last column - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:255:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 255 | finger1 = col_; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'typename seqan::Iterator, const seqan::Tag >::Type seqan::_smithWatermanTrace(seqan::Gaps&, seqan::Gaps&, typename seqan::LocalAlignmentFinder::TBoolMatrix&, seqan::Iter, seqan::CountingIteratorImpl_ > >, const seqan::Score&) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; unsigned int DIMENSION = 0; typename seqan::Iterator, const seqan::Tag >::Type = seqan::Iter, seqan::CountingIteratorImpl_ > >; typename seqan::LocalAlignmentFinder::TBoolMatrix = seqan::String]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:714:37: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:595:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 595 | it_ = source_; - | ~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h: In instantiation of 'void seqan::_smithWatermanDeclump(seqan::LocalAlignmentFinder&, seqan::Gaps&, seqan::Gaps&, const seqan::Score&) [with TScoreValue = int; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:736:26: required from 'TScoreValue seqan::_smithWatermanGetNext(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:107:37: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:445:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 445 | finger1 = end_col; //points to last column - | ~~~~~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:189, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:447:17: warning: implicitly-declared 'constexpr seqan::Iter, seqan::CountingIteratorImpl_ > >& seqan::Iter, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 447 | finger0 = end_col; - | ~~~~~~~~^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::Matrix]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 647 | return Iter >(container(left), hostIterator(left) - right); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:22: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:369:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:37: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:647:12: required from 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:215:44: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:520:23: required from 'typename seqan::Iterator >::Type seqan::end(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:504:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(const T&) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:216:33: required from 'TScoreValue seqan::_smithWatermanGetMatrix(seqan::LocalAlignmentFinder&, const TStringH&, const TStringV&, const seqan::Score&, TScoreValue) [with TScoreValue = int; TScoreSpec = seqan::Tag; TStringH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TStringV = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_waterman_eggert_impl.h:703:46: required from 'TScoreValue seqan::_smithWaterman(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentFinder&, const seqan::Score&, TScoreValue) [with TSourceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSourceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:105:30: required from 'bool seqan::nextLocalAlignment(seqan::Gaps&, seqan::Gaps&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/local_alignment_enumeration_unbanded.h:117:30: required from 'bool seqan::nextLocalAlignment(seqan::Align&, seqan::LocalAlignmentEnumerator, seqan::Tag >&) [with TScoreValue = int; TScoreSpec = seqan::Tag; TSequence = seqan::String, seqan::Alloc<> >; TAlignSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:34:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:486:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 486 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_local.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 58%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_index -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/tutorial/pattern_matching/find_index.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_index -lrt -lz -lbz2 +[ 59%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/tutorial/sam_and_bam_io/solution2.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_2_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/link.txt --verbose=1 -[ 58%] Built target demo_tutorial_pattern_matching_find_index -make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/tutorial/sequences/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_sequences_assignment_2_solution -lrt -lz -lbz2 +[ 59%] Built target demo_tutorial_sam_and_bam_io_solution2 +make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/depend.internal". -Scanning dependencies of target demo_dox_index_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend.internal". +Scanning dependencies of target demo_dox_align_gaps_example make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/build +make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/gaps_example.cpp +[ 59%] Linking CXX executable ../bin/demo_dox_graph_algorithms_all_pairs_shortest_path +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o -o ../bin/demo_dox_graph_algorithms_all_pairs_shortest_path -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Building CXX object demos/CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/finder.cpp -[ 58%] Built target demo_tutorial_sequences_assignment_2_solution -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend +[ 59%] Built target demo_dox_graph_algorithms_all_pairs_shortest_path +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_file_speed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_final_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/file_speed.cpp +[ 59%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/final_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, @@ -86246,22 +86340,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 58%] Linking CXX executable ../bin/demo_dox_graph_algorithms_all_pairs_shortest_path -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/dox/graph_algorithms/all_pairs_shortest_path.cpp.o -o ../bin/demo_dox_graph_algorithms_all_pairs_shortest_path -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Built target demo_dox_graph_algorithms_all_pairs_shortest_path -make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/depend.internal". -Scanning dependencies of target demo_dox_find_finder_online -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_online.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/index/finder.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -86271,6 +86349,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 59%] Linking CXX executable ../bin/demo_dox_index_open_save +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_open_save.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_open_save.dir/dox/index/open_save.cpp.o -o ../bin/demo_dox_index_open_save -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -86293,59 +86374,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index > >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String >; TSpec = void]' 429 | Index(Index const &other): | ^~~~~ -[ 59%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_interval_tree -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/interval_tree.cpp -[ 59%] Linking CXX executable ../bin/demo_dox_index_finder -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_finder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o -o ../bin/demo_dox_index_finder -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Built target demo_dox_index_finder -make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend.internal". -Scanning dependencies of target demo_dox_align_gaps_example -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Building CXX object demos/CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/gaps_example.cpp -[ 60%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_speed -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_speed.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o -o ../bin/demo_unassigned_or_unused_file_speed -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_unassigned_or_unused_file_speed -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_final_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/final_solution.cpp -[ 60%] Linking CXX executable ../bin/demo_dox_find_finder_online -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_online.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o -o ../bin/demo_dox_find_finder_online -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_find_finder_online +[ 59%] Built target demo_dox_index_open_save make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/DependInfo.cmake --color= @@ -86355,8 +86385,27 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/dox/index/UNUSED_shape.cpp.o +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/dox/index/UNUSED_shape.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_UNUSED_shape.dir/dox/index/UNUSED_shape.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape.cpp +[ 59%] Linking CXX executable ../bin/demo_dox_index_mums +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_mums.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_mums.dir/dox/index/mums.cpp.o -o ../bin/demo_dox_index_mums -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Built target demo_dox_index_mums +make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_strongly_connected_components +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/strongly_connected_components.cpp +[ 59%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/tutorial/pairwise_sequence_alignment/alignment_local.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_local -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/interval_tree.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::addInterval(TGraph&, TPropertyMap&, TInterval) [with TGraph = seqan::Graph > >; TPropertyMap = seqan::String > >, seqan::StorePointsOnly>, seqan::Alloc<> >; TInterval = seqan::IntervalAndCargo > >]': @@ -86491,27 +86540,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > >, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable ../bin/demo_dox_graph_algorithms_longest_common_subsequence -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_longest_common_subsequence -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_graph_algorithms_longest_common_subsequence -make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend -[ 60%] Linking CXX executable ../bin/demo_dox_bam_io_bam_tags_dict -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o -o ../bin/demo_dox_bam_io_bam_tags_dict -lrt -lz -lbz2 -Scanning dependencies of target demo_dox_graph_algorithms_strongly_connected_components -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/strongly_connected_components.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_bam_io_bam_tags_dict +[ 59%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local make -f demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/DependInfo.cmake --color= @@ -86521,22 +86551,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/dox/graph_types/graph_algo_dijkstra.cpp.o +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/dox/graph_types/graph_algo_dijkstra.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/dox/graph_types/graph_algo_dijkstra.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_types/graph_algo_dijkstra.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 60%] Linking CXX executable ../bin/demo_dox_align_gaps_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_gaps_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o -o ../bin/demo_dox_align_gaps_example -lrt -lz -lbz2 +[ 59%] Linking CXX executable ../bin/demo_dox_find_finder_online +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_online.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_online.dir/dox/find/finder_online.cpp.o -o ../bin/demo_dox_find_finder_online -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_align_gaps_example +[ 59%] Built target demo_dox_find_finder_online make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/DependInfo.cmake --color= @@ -86546,13 +86567,13 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/tutorial/a_first_example/example_tags.cpp.o +[ 59%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/tutorial/a_first_example/example_tags.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/tutorial/a_first_example/example_tags.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/example_tags.cpp -[ 60%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tags +[ 59%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tags cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/tutorial/a_first_example/example_tags.cpp.o -o ../bin/demo_tutorial_a_first_example_example_tags -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_tutorial_a_first_example_example_tags +[ 59%] Built target demo_tutorial_a_first_example_example_tags make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/DependInfo.cmake --color= @@ -86562,13 +86583,16 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/tutorial/gff_and_gtf_io/solution3.cpp.o +[ 59%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/tutorial/gff_and_gtf_io/solution3.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/tutorial/gff_and_gtf_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution3.cpp -[ 60%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape.dir/dox/index/UNUSED_shape.cpp.o -o ../bin/demo_dox_index_UNUSED_shape -lrt -lz -lbz2 +[ 59%] Linking CXX executable ../bin/demo_unassigned_or_unused_segmentalignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/unassigned_or_unused/segmentalignment.cpp.o -o ../bin/demo_unassigned_or_unused_segmentalignment -lrt -lz -lbz2 +[ 59%] Linking CXX executable ../bin/demo_dox_index_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_finder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_finder.dir/dox/index/finder.cpp.o -o ../bin/demo_dox_index_finder -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_index_UNUSED_shape +[ 59%] Built target demo_dox_index_finder make -f demos/CMakeFiles/demo_dox_index_iterator_short.dir/build.make demos/CMakeFiles/demo_dox_index_iterator_short.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator_short.dir/DependInfo.cmake --color= @@ -86578,56 +86602,162 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_iterator_short.dir/build.make demos/CMakeFiles/demo_dox_index_iterator_short.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_dox_index_iterator_short.dir/dox/index/iterator_short.cpp.o +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_index_iterator_short.dir/dox/index/iterator_short.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_iterator_short.dir/dox/index/iterator_short.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator_short.cpp -[ 60%] Linking CXX executable ../bin/demo_dox_graph_types_graph_algo_dijkstra -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/dox/graph_types/graph_algo_dijkstra.cpp.o -o ../bin/demo_dox_graph_types_graph_algo_dijkstra -lrt -lz -lbz2 -[ 60%] Linking CXX executable ../bin/demo_dox_graph_algorithms_strongly_connected_components -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/link.txt --verbose=1 -[ 60%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_interval_tree -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o -o ../bin/demo_dox_graph_algorithms_strongly_connected_components -lrt -lz -lbz2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_interval_tree -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_tutorial_simple_rna_seq_interval_tree +[ 59%] Built target demo_unassigned_or_unused_segmentalignment make -f demos/CMakeFiles/demo_dox_sequence_string.dir/build.make demos/CMakeFiles/demo_dox_sequence_string.dir/depend -[ 60%] Built target demo_dox_graph_algorithms_strongly_connected_components make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/depend +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/depend.internal". +Scanning dependencies of target demo_dox_sequence_string make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_string.dir/build.make demos/CMakeFiles/demo_dox_sequence_string.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Building CXX object demos/CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/string.cpp +[ 60%] Linking CXX executable ../bin/demo_unassigned_or_unused_file_speed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_file_speed.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_file_speed.dir/unassigned_or_unused/file_speed.cpp.o -o ../bin/demo_unassigned_or_unused_file_speed -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 60%] Built target demo_unassigned_or_unused_file_speed +make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/depend.internal". -[ 60%] Built target demo_dox_graph_types_graph_algo_dijkstra +Scanning dependencies of target demo_tutorial_fragment_store_display_aligned_reads +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 60%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/display_aligned_reads.cpp +[ 60%] Linking CXX executable ../bin/demo_dox_align_gaps_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_gaps_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_gaps_example.dir/dox/align/gaps_example.cpp.o -o ../bin/demo_dox_align_gaps_example -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 60%] Built target demo_dox_align_gaps_example make -f demos/CMakeFiles/demo_dox_align_integrate_align.dir/build.make demos/CMakeFiles/demo_dox_align_integrate_align.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_string -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_string.dir/build.make demos/CMakeFiles/demo_dox_sequence_string.dir/build Scanning dependencies of target demo_dox_align_integrate_align make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_align_integrate_align.dir/build.make demos/CMakeFiles/demo_dox_align_integrate_align.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/integrate_align.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 61%] Linking CXX executable ../bin/demo_dox_bam_io_bam_tags_dict +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/dox/bam_io/bam_tags_dict.cpp.o -o ../bin/demo_dox_bam_io_bam_tags_dict -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_dox_bam_io_bam_tags_dict +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_fragment_store_display_aligned_reads +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_solution_4_templateSubclassing make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Building CXX object demos/CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/string.cpp -[ 61%] Building CXX object demos/CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/integrate_align.cpp -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/display_aligned_reads.cpp +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_4_templateSubclassing.cpp +[ 61%] Linking CXX executable ../bin/demo_dox_graph_algorithms_longest_common_subsequence +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/dox/graph_algorithms/longest_common_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_longest_common_subsequence -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape.dir/dox/index/UNUSED_shape.cpp.o -o ../bin/demo_dox_index_UNUSED_shape -lrt -lz -lbz2 +[ 61%] Built target demo_dox_graph_algorithms_longest_common_subsequence +make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_dox_index_UNUSED_shape +make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend.internal". +Scanning dependencies of target demo_dox_bam_io_bam_file_in +Scanning dependencies of target demo_dox_align_extend_extend_alignment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build +make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_extend/extend_alignment.cpp +[ 61%] Building CXX object demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp +[ 61%] Linking CXX executable ../bin/demo_dox_graph_types_graph_algo_dijkstra +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/dox/graph_types/graph_algo_dijkstra.cpp.o -o ../bin/demo_dox_graph_types_graph_algo_dijkstra -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_dox_graph_types_graph_algo_dijkstra +make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend.internal". +Scanning dependencies of target demo_tutorial_blast_io_read_assignment +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp +[ 61%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_interval_tree +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/tutorial/simple_rna_seq/interval_tree.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_interval_tree -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_tutorial_simple_rna_seq_interval_tree +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend.internal". +[ 61%] Linking CXX executable ../bin/demo_dox_graph_algorithms_strongly_connected_components +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/dox/graph_algorithms/strongly_connected_components.cpp.o -o ../bin/demo_dox_graph_algorithms_strongly_connected_components -lrt -lz -lbz2 +[ 61%] Linking CXX executable ../bin/demo_dox_sequence_string +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_string.dir/link.txt --verbose=1 +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o -o ../bin/demo_dox_sequence_string -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_dox_graph_algorithms_strongly_connected_components +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_dox_sequence_string +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator_short.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -86637,6 +86767,18 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +Scanning dependencies of target demo_tutorial_vcf_io_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_index_iterators_index_property_maps +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/tutorial/index_iterators/index_property_maps.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/tutorial/index_iterators/index_property_maps.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator_short.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks; TDfsOrder = seqan::Postorder_]': @@ -86761,9 +86903,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 61%] Linking CXX executable ../bin/demo_dox_index_getOccurrences_getFrequency_range_getFibre -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o -o ../bin/demo_dox_index_getOccurrences_getFrequency_range_getFibre -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, @@ -86927,35 +87066,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_dox_index_getOccurrences_getFrequency_range_getFibre -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/DependInfo.cmake --color= -[ 61%] Linking CXX executable ../bin/demo_dox_sequence_string -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_string.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_string.dir/dox/sequence/string.cpp.o -o ../bin/demo_dox_sequence_string -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_a_first_example_solution_4_templateSubclassing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_4_templateSubclassing.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_dox_sequence_string -make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend.internal". -Scanning dependencies of target demo_dox_align_extend_extend_alignment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_extend/extend_alignment.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/display_aligned_reads.cpp:3: @@ -87097,6 +87207,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 61%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -87135,6 +87247,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/tutorial/gff_and_gtf_io/solution3.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/display_aligned_reads.cpp:3: @@ -87154,6 +87267,59 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 61%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_4_templateSubclassing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_4_templateSubclassing -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_tutorial_gff_and_gtf_io_solution3 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_tutorial_a_first_example_solution_4_templateSubclassing +make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp +Scanning dependencies of target demo_tabix_io_tabix_vcf +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 62%] Building CXX object demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:8:84: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -87184,6 +87350,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:8:84: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -87215,12 +87401,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 61%] Linking CXX executable ../bin/demo_dox_index_iterator_short -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_iterator_short.dir/link.txt --verbose=1 -[ 61%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_iterator_short.dir/dox/index/iterator_short.cpp.o -o ../bin/demo_dox_index_iterator_short -lrt -lz -lbz2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/tutorial/gff_and_gtf_io/solution3.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -87390,51 +87570,136 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 62%] Linking CXX executable ../bin/demo_dox_index_iterator_short +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_iterator_short.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_iterator_short.dir/dox/index/iterator_short.cpp.o -o ../bin/demo_dox_index_iterator_short -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_tutorial_gff_and_gtf_io_solution3 -make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend -[ 61%] Built target demo_dox_index_iterator_short -make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend.internal". -Scanning dependencies of target demo_tutorial_blast_io_read_assignment -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp -Scanning dependencies of target demo_dox_bam_io_bam_file_in -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp -[ 61%] Linking CXX executable ../bin/demo_dox_consensus_consensus_alignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_consensus_consensus_alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o -o ../bin/demo_dox_consensus_consensus_alignment -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_dox_consensus_consensus_alignment -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:56, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:56, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 62%] Built target demo_dox_index_iterator_short +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend.internal". +Scanning dependencies of target demo_dox_basic_metaprogramming_switch make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp -[ 61%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_4_templateSubclassing -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/tutorial/a_first_example/solution_4_templateSubclassing.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_4_templateSubclassing -lrt -lz -lbz2 +[ 62%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_switch.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:21:46: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:42, @@ -87446,22 +87711,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_tutorial_a_first_example_solution_4_templateSubclassing -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_property_maps -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/tutorial/index_iterators/index_property_maps.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/tutorial/index_iterators/index_property_maps.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp -[ 61%] Linking CXX executable ../bin/demo_tutorial_fragment_store_access_aligned_reads2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o -o ../bin/demo_tutorial_fragment_store_access_aligned_reads2 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, @@ -87521,6 +87779,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align_extend.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/align_extend/extend_alignment.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/align_extend/align_extend.h: In instantiation of 'TScoreValue seqan::_extendAlignmentImpl(seqan::Gaps&, seqan::Gaps&, const TScoreValue&, const TString0&, const TString1&, const seqan::Tuple&, const seqan::ExtensionDirection&, int, int, const TScoreValue&, const seqan::Score&, const TBoolBanded&, const TBoolXDrop&, TAliExtContext_&) [with TSource0 = seqan::Segment >, seqan::InfixSegment>; TSource1 = seqan::Segment >, seqan::InfixSegment>; TGapsSpec0 = seqan::Tag; TGapsSpec1 = seqan::Tag; TString0 = seqan::String >; TString1 = seqan::String >; TPos = unsigned int; TScoreValue = int; TScoreSpec = seqan::Tag; TBoolBanded = seqan::True; TBoolXDrop = seqan::True; TAliExtContext_ = seqan::AliExtContext_ >, seqan::InfixSegment>, seqan::Tag >, seqan::Gaps >, seqan::InfixSegment>, seqan::Tag >, seqan::DPContext >, unsigned char, seqan::String >, seqan::Alloc<> >, seqan::String > >]': @@ -87589,6 +87865,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -87610,6 +87912,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:55, @@ -87662,6 +87984,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -87693,9 +88042,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_tutorial_fragment_store_access_aligned_reads2 -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:30:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::Terminator_ > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix >, seqan::Tag >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::AlignExtend_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String, seqan::Alloc<> >; TScoutState = seqan::DPScoutState_ > >; TSequenceH = seqan::Segment >, seqan::InfixSegment>; TSequenceV = seqan::Segment >, seqan::InfixSegment>; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::AlignExtend_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn<>; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' @@ -87723,16 +88096,65 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend.internal". -[ 61%] Linking CXX executable ../bin/demo_dox_align_integrate_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_integrate_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o -o ../bin/demo_dox_align_integrate_align -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_vcf_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 62%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_switch +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o -o ../bin/demo_dox_basic_metaprogramming_switch -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:30:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:61, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/demos/dox/align_extend/extend_alignment.cpp:3: @@ -87763,9 +88185,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:117:53: note: initializing argument 1 of 'seqan::ModifiedString::ModifiedString(typename seqan::Parameter_::Type) [with THost = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 117 | ModifiedString(typename Parameter_::Type host) : | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 62%] Built target demo_dox_basic_metaprogramming_switch +make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +Scanning dependencies of target demo_dox_align_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 63%] Building CXX object demos/CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/align.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, + from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:18:31: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, @@ -87832,379 +88305,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:56, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:56, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::BlastTabular_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = seqan::BlastIOContext<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:21:46: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/blast.h:54, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/blast_io/read_assignment.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_dox_align_integrate_align -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/bam_io/bam_file_in.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:8:84: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:8:84: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:30:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:30:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:18:31: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:40:98: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_property_maps.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution1.cpp:2: @@ -88231,23 +88347,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 66 | itGapsPattern = begin(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 67 | itGapsEnd = end(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -88298,116 +88397,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 61%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_property_maps +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 66 | itGapsPattern = begin(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 67 | itGapsEnd = end(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +[ 63%] Linking CXX executable ../bin/demo_dox_align_integrate_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_integrate_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_integrate_align.dir/dox/align/integrate_align.cpp.o -o ../bin/demo_dox_align_integrate_align -lrt -lz -lbz2 +[ 63%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_property_maps cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/tutorial/index_iterators/index_property_maps.cpp.o -o ../bin/demo_tutorial_index_iterators_index_property_maps -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_tutorial_index_iterators_index_property_maps -make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend.internal". -Scanning dependencies of target demo_tabix_io_tabix_vcf -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 62%] Building CXX object demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:48, - from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:18:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/vcf_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 62%] Linking CXX executable ../bin/demo_unassigned_or_unused_benchmark_stream -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o -o ../bin/demo_unassigned_or_unused_benchmark_stream -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:18:31: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tabix_io/tabix_vcf.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 62%] Built target demo_unassigned_or_unused_benchmark_stream -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend.internal". -Scanning dependencies of target demo_dox_basic_metaprogramming_switch -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 62%] Building CXX object demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/metaprogramming_switch.cpp -[ 62%] Linking CXX executable ../bin/demo_dox_basic_metaprogramming_switch -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/dox/basic/metaprogramming_switch.cpp.o -o ../bin/demo_dox_basic_metaprogramming_switch -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 62%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution1.dir/link.txt --verbose=1 -[ 62%] Built target demo_dox_basic_metaprogramming_switch -make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o -o ../bin/demo_tutorial_vcf_io_solution1 -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/depend.internal". -Scanning dependencies of target demo_dox_align_align -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Building CXX object demos/CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/align.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_tutorial_vcf_io_solution1 +[ 63%] Built target demo_dox_align_integrate_align make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_gff2gtf -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/gff2gtf.cpp -[ 63%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_final_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_final_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_tutorial_parsing_command_line_arguments_final_solution +[ 63%] Built target demo_tutorial_index_iterators_index_property_maps make -f demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build.make demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/depend.internal". Scanning dependencies of target demo_dox_arg_parse_argument_parser @@ -88415,23 +88439,45 @@ make -f demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build.make demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 63%] Building CXX object demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/dox/arg_parse/argument_parser.cpp.o +Scanning dependencies of target demo_unassigned_or_unused_gff2gtf cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_arg_parse_argument_parser.dir/dox/arg_parse/argument_parser.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/arg_parse/argument_parser.cpp -[ 63%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step5 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 +make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 63%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/gff2gtf.cpp +[ 63%] Linking CXX executable ../bin/demo_dox_index_getOccurrences_getFrequency_range_getFibre +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.o -o ../bin/demo_dox_index_getOccurrences_getFrequency_range_getFibre -lrt -lz -lbz2 +[ 63%] Linking CXX executable ../bin/demo_tutorial_vcf_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_solution1.dir/tutorial/vcf_io/solution1.cpp.o -o ../bin/demo_tutorial_vcf_io_solution1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 63%] Built target demo_dox_index_getOccurrences_getFrequency_range_getFibre make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/depend.internal". +[ 63%] Built target demo_tutorial_vcf_io_solution1 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend.internal". Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_a_first_example_solution_4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 63%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/tutorial/parsing_command_line_arguments/example1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/tutorial/parsing_command_line_arguments/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example1.cpp +[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_4.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -88561,43 +88607,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 63%] Linking CXX executable ../bin/demo_dox_align_extend_extend_alignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_extend_extend_alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o -o ../bin/demo_dox_align_extend_extend_alignment -lrt -lz -lbz2 -[ 63%] Linking CXX executable ../bin/demo_dox_bam_io_bam_file_in -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bam_io_bam_file_in.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o -o ../bin/demo_dox_bam_io_bam_file_in -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Linking CXX executable ../bin/demo_tutorial_fragment_store_access_aligned_reads2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/tutorial/fragment_store/access_aligned_reads2.cpp.o -o ../bin/demo_tutorial_fragment_store_access_aligned_reads2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_dox_align_extend_extend_alignment -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend -[ 63%] Built target demo_dox_bam_io_bam_file_in +[ 64%] Built target demo_tutorial_fragment_store_access_aligned_reads2 make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/depend.internal". Scanning dependencies of target demo_dox_gff_io_UNUSED_gff_stream_read make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_a_first_example_solution_4 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Building CXX object demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/dox/gff_io/UNUSED_gff_stream_read.cpp.o +[ 64%] Building CXX object demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/dox/gff_io/UNUSED_gff_stream_read.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/dox/gff_io/UNUSED_gff_stream_read.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/gff_io/UNUSED_gff_stream_read.cpp -[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_4.cpp -[ 64%] Linking CXX executable ../bin/demo_tabix_io_tabix_vcf -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tabix_io_tabix_vcf.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o -o ../bin/demo_tabix_io_tabix_vcf -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/tutorial/pairwise_sequence_alignment/assignment5_step5.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step5 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_tabix_io_tabix_vcf +[ 64%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 make -f demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/DependInfo.cmake --color= @@ -88609,6 +88639,54 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/dox/graph_algorithms/dag_shortest_path.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/dox/graph_algorithms/dag_shortest_path.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/dag_shortest_path.cpp +[ 64%] Linking CXX executable ../bin/demo_dox_align_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o -o ../bin/demo_dox_align_align -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_tabix_io_tabix_vcf +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tabix_io_tabix_vcf.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tabix_io_tabix_vcf.dir/tabix_io/tabix_vcf.cpp.o -o ../bin/demo_tabix_io_tabix_vcf -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_dox_align_align +make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_dijkstra +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_tabix_io_tabix_vcf +make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake --color= +[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/dijkstra.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_floyd_warshall_algorithm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp +[ 64%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_4 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_tutorial_a_first_example_solution_4 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_ford_fulkerson_algorithm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, from /build/seqan2-2.4.0+dfsg/demos/dox/gff_io/UNUSED_gff_stream_read.cpp:2: @@ -88681,94 +88759,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 64%] Linking CXX executable ../bin/demo_dox_align_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_align.dir/dox/align/align.cpp.o -o ../bin/demo_dox_align_align -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_align_align -make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_dijkstra -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/dijkstra.cpp -[ 64%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/tutorial/a_first_example/solution_4.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_4 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_tutorial_a_first_example_solution_4 -make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_floyd_warshall_algorithm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp -[ 64%] Linking CXX executable ../bin/demo_tutorial_blast_io_read_assignment -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o -o ../bin/demo_tutorial_blast_io_read_assignment -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution1 -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_dag_shortest_path -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/dox/graph_algorithms/dag_shortest_path.cpp.o -o ../bin/demo_dox_graph_algorithms_dag_shortest_path -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_dox_bam_io_bam_file_in +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_bam_io_bam_file_in.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_bam_io_bam_file_in.dir/dox/bam_io/bam_file_in.cpp.o -o ../bin/demo_dox_bam_io_bam_file_in -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_graph_algorithms_dag_shortest_path -make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend +[ 64%] Built target demo_dox_bam_io_bam_file_in +make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_ford_fulkerson_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_segments make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_segments.cpp +[ 64%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_final_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/tutorial/parsing_command_line_arguments/final_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_final_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_tutorial_blast_io_read_assignment -make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake --color= -[ 64%] Built target demo_tutorial_simple_rna_seq_genequant_solution1 +[ 64%] Built target demo_tutorial_parsing_command_line_arguments_final_solution make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_example_segments -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build Scanning dependencies of target demo_dox_stream_lexical_cast -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_segments.cpp [ 64%] Building CXX object demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/dox/stream/lexical_cast.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_stream_lexical_cast.dir/dox/stream/lexical_cast.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/stream/lexical_cast.cpp -[ 64%] Linking CXX executable ../bin/demo_tutorial_fragment_store_display_aligned_reads -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o -o ../bin/demo_tutorial_fragment_store_display_aligned_reads -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_floyd_warshall_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/link.txt --verbose=1 +[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_dag_shortest_path +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/dox/graph_algorithms/dag_shortest_path.cpp.o -o ../bin/demo_dox_graph_algorithms_dag_shortest_path -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_floyd_warshall_algorithm -lrt -lz -lbz2 -[ 64%] Built target demo_tutorial_fragment_store_display_aligned_reads +[ 64%] Built target demo_dox_graph_algorithms_dag_shortest_path make -f demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build.make demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/DependInfo.cmake --color= @@ -88780,6 +88807,9 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/dox/misc/name_store_cache.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_name_store_cache.dir/dox/misc/name_store_cache.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/name_store_cache.cpp +[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_floyd_warshall_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/dox/graph_algorithms/floyd_warshall_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_floyd_warshall_algorithm -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Built target demo_dox_graph_algorithms_floyd_warshall_algorithm make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/depend @@ -88793,11 +88823,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp -[ 64%] Linking CXX executable ../bin/demo_dox_gff_io_UNUSED_gff_stream_read -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/dox/gff_io/UNUSED_gff_stream_read.cpp.o -o ../bin/demo_dox_gff_io_UNUSED_gff_stream_read -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_dox_align_extend_extend_alignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_extend_extend_alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_extend_extend_alignment.dir/dox/align_extend/extend_alignment.cpp.o -o ../bin/demo_dox_align_extend_extend_alignment -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_gff_io_UNUSED_gff_stream_read +[ 64%] Built target demo_dox_align_extend_extend_alignment make -f demos/CMakeFiles/demo_howto_scores_init_score.dir/build.make demos/CMakeFiles/demo_howto_scores_init_score.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_init_score.dir/DependInfo.cmake --color= @@ -88809,30 +88839,27 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_howto_scores_init_score.dir/howto/scores/init_score.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_scores_init_score.dir/howto/scores/init_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/scores/init_score.cpp -[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_dijkstra -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o -o ../bin/demo_dox_graph_algorithms_dijkstra -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_tutorial_sequences_example_segments +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_segments.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o -o ../bin/demo_tutorial_sequences_example_segments -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_graph_algorithms_dijkstra +[ 64%] Built target demo_tutorial_sequences_example_segments make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/depend.internal". +[ 64%] Linking CXX executable ../bin/demo_unassigned_or_unused_benchmark_stream +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/unassigned_or_unused/benchmark_stream.cpp.o -o ../bin/demo_unassigned_or_unused_benchmark_stream -lrt -lz -lbz2 Scanning dependencies of target demo_dox_graph_algorithms_heaviest_increasing_subsequence make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/dox/graph_algorithms/heaviest_increasing_subsequence.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/dox/graph_algorithms/heaviest_increasing_subsequence.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp -[ 64%] Linking CXX executable ../bin/demo_tutorial_sequences_example_segments -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_segments.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_segments.dir/tutorial/sequences/example_segments.cpp.o -o ../bin/demo_tutorial_sequences_example_segments -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_dox_stream_lexical_cast -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_stream_lexical_cast.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_stream_lexical_cast.dir/dox/stream/lexical_cast.cpp.o -o ../bin/demo_dox_stream_lexical_cast -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_tutorial_sequences_example_segments +[ 64%] Built target demo_unassigned_or_unused_benchmark_stream make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/DependInfo.cmake --color= @@ -88842,36 +88869,45 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_ford_fulkerson_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/link.txt --verbose=1 [ 64%] Building CXX object demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/dox/align_profile/profile_seq_score.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/dox/align_profile/profile_seq_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_ford_fulkerson_algorithm -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_dox_stream_lexical_cast +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_stream_lexical_cast.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_stream_lexical_cast.dir/dox/stream/lexical_cast.cpp.o -o ../bin/demo_dox_stream_lexical_cast -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_stream_lexical_cast +[ 64%] Built target demo_dox_graph_algorithms_ford_fulkerson_algorithm make -f demos/CMakeFiles/demo_dox_index_mummy.dir/build.make demos/CMakeFiles/demo_dox_index_mummy.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/DependInfo.cmake --color= +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_dox_stream_lexical_cast Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/depend.internal". +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_conversions_copy +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_dox_index_mummy make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_mummy.dir/build.make demos/CMakeFiles/demo_dox_index_mummy.dir/build +[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_copy.cpp make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_index_mummy.dir/dox/index/mummy.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_mummy.dir/dox/index/mummy.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp -[ 64%] Linking CXX executable ../bin/demo_unassigned_or_unused_gff2gtf -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o -o ../bin/demo_unassigned_or_unused_gff2gtf -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_ford_fulkerson_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_ford_fulkerson_algorithm -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_graph_algorithms_ford_fulkerson_algorithm -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/DependInfo.cmake --color= +[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_dijkstra +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/dox/graph_algorithms/dijkstra.cpp.o -o ../bin/demo_dox_graph_algorithms_dijkstra -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend.internal". -[ 64%] Built target demo_unassigned_or_unused_gff2gtf +[ 64%] Built target demo_dox_graph_algorithms_dijkstra make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/DependInfo.cmake --color= @@ -88880,23 +88916,14 @@ Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment6_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build -Scanning dependencies of target demo_tutorial_sequences_example_conversions_copy -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/tutorial/parsing_command_line_arguments/assignment6_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/tutorial/parsing_command_line_arguments/assignment6_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment6_solution.cpp -[ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_copy.cpp -[ 64%] Linking CXX executable ../bin/demo_dox_misc_name_store_cache -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_name_store_cache.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_name_store_cache.dir/dox/misc/name_store_cache.cpp.o -o ../bin/demo_dox_misc_name_store_cache -lrt -lz -lbz2 -[ 64%] Linking CXX executable ../bin/demo_howto_scores_init_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_scores_init_score.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_scores_init_score.dir/howto/scores/init_score.cpp.o -o ../bin/demo_howto_scores_init_score -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_dox_consensus_consensus_alignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_consensus_consensus_alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_consensus_consensus_alignment.dir/dox/consensus/consensus_alignment.cpp.o -o ../bin/demo_dox_consensus_consensus_alignment -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_howto_scores_init_score +[ 64%] Built target demo_dox_consensus_consensus_alignment make -f demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/DependInfo.cmake --color= @@ -88908,8 +88935,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/dox/graph_algorithms/breadth_first_search.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/dox/graph_algorithms/breadth_first_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/breadth_first_search.cpp +[ 64%] Linking CXX executable ../bin/demo_dox_gff_io_UNUSED_gff_stream_read +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/dox/gff_io/UNUSED_gff_stream_read.cpp.o -o ../bin/demo_dox_gff_io_UNUSED_gff_stream_read -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_misc_name_store_cache +[ 64%] Built target demo_dox_gff_io_UNUSED_gff_stream_read make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/DependInfo.cmake --color= @@ -88921,20 +88951,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/dox/graph_algorithms/longest_increasing_subsequence.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/dox/graph_algorithms/longest_increasing_subsequence.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/longest_increasing_subsequence.cpp -[ 64%] Linking CXX executable ../bin/demo_dox_graph_algorithms_heaviest_increasing_subsequence -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/dox/graph_algorithms/heaviest_increasing_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_heaviest_increasing_subsequence -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 64%] Linking CXX executable ../bin/demo_dox_misc_name_store_cache +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_name_store_cache.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_name_store_cache.dir/dox/misc/name_store_cache.cpp.o -o ../bin/demo_dox_misc_name_store_cache -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_graph_algorithms_heaviest_increasing_subsequence +[ 64%] Built target demo_dox_misc_name_store_cache make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/DependInfo.cmake --color= @@ -88946,11 +88967,72 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 64%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/tutorial/a_first_example/solution_6.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/tutorial/a_first_example/solution_6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/solution_6.cpp +[ 64%] Linking CXX executable ../bin/demo_howto_scores_init_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_scores_init_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_scores_init_score.dir/howto/scores/init_score.cpp.o -o ../bin/demo_howto_scores_init_score -lrt -lz -lbz2 +[ 64%] Linking CXX executable ../bin/demo_tutorial_blast_io_read_assignment +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/tutorial/blast_io/read_assignment.cpp.o -o ../bin/demo_tutorial_blast_io_read_assignment -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_howto_scores_init_score +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_tutorial_blast_io_read_assignment +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend.internal". +Scanning dependencies of target demo_tutorial_bed_io_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution3.cpp +[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_heaviest_increasing_subsequence +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/dox/graph_algorithms/heaviest_increasing_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_heaviest_increasing_subsequence -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_dox_graph_algorithms_heaviest_increasing_subsequence +make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend.internal". +Scanning dependencies of target demo_dox_seeds_seeds_chaining +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_chaining.cpp +[ 65%] Linking CXX executable ../bin/demo_unassigned_or_unused_gff2gtf +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/unassigned_or_unused/gff2gtf.cpp.o -o ../bin/demo_unassigned_or_unused_gff2gtf -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_unassigned_or_unused_gff2gtf +make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend.internal". +Scanning dependencies of target demo_dox_seeds_seeds_extension +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_extension.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -88958,6 +89040,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 65%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/tutorial/simple_rna_seq/genequant_solution1.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_tutorial_simple_rna_seq_genequant_solution1 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend.internal". +Scanning dependencies of target demo_dox_graph_algorithms_prims_algorithm +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/prims_algorithm.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_copy.cpp:2: @@ -88982,6 +89080,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 65%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_copy.cpp:2: @@ -89007,6 +89108,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats +make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend.internal". +Scanning dependencies of target demo_dox_index_find_repeats +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_conversions_copy.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -89024,91 +89136,52 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 64%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/unassigned_or_unused/tutorial_file_io/stream_compression_formats.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, +[ 65%] Building CXX object demos/CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp +[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_breadth_first_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/dox/graph_algorithms/breadth_first_search.cpp.o -o ../bin/demo_dox_graph_algorithms_breadth_first_search -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_dox_graph_algorithms_breadth_first_search +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp +[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_longest_increasing_subsequence +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/dox/graph_algorithms/longest_increasing_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_longest_increasing_subsequence -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_dox_graph_algorithms_longest_increasing_subsequence +make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend.internal". +Scanning dependencies of target demo_dox_seeds_seeds_add_seed +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_add_seed.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -89136,19 +89209,55 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 65%] Linking CXX executable ../bin/demo_tutorial_sequences_example_conversions_copy +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o -o ../bin/demo_tutorial_sequences_example_conversions_copy -lrt -lz -lbz2 +[ 65%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_6 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/tutorial/a_first_example/solution_6.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_6 -lrt -lz -lbz2 +[ 65%] Built target demo_tutorial_sequences_example_conversions_copy +make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend.internal". +Scanning dependencies of target demo_tutorial_graph_graph_hmm make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build +make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp +[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_hmm.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_tutorial_a_first_example_solution_6 +make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/depend.internal". +Scanning dependencies of target demo_dox_index_iterator +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 66%] Building CXX object demos/CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 66 | itGapsPattern = begin(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 67 | itGapsEnd = end(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -89177,6 +89286,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 66%] Linking CXX executable ../bin/demo_tutorial_fragment_store_display_aligned_reads +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/tutorial/fragment_store/display_aligned_reads.cpp.o -o ../bin/demo_tutorial_fragment_store_display_aligned_reads -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -89253,6 +89365,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 66%] Built target demo_tutorial_fragment_store_display_aligned_reads +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alphabets_example_size +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_size.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -89300,8 +89425,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = long long unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ -[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_longest_increasing_subsequence -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::Owner<> >, seqan::IndexEsa<> >; TSpec = seqan::BottomUp<>]': @@ -89320,7 +89443,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/dox/graph_algorithms/longest_increasing_subsequence.cpp.o -o ../bin/demo_dox_graph_algorithms_longest_increasing_subsequence -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -89379,70 +89501,345 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_breadth_first_search +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_chaining.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:44, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_extension.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 66%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_size +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_size.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o -o ../bin/demo_tutorial_alphabets_example_size -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/dox/graph_algorithms/breadth_first_search.cpp.o -o ../bin/demo_dox_graph_algorithms_breadth_first_search -lrt -lz -lbz2 -[ 65%] Built target demo_dox_graph_algorithms_longest_increasing_subsequence -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend +[ 66%] Built target demo_tutorial_alphabets_example_size +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_bed_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend.internal". +Scanning dependencies of target demo_dox_index_UNUSED_shape_hash_next make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution3.cpp -[ 65%] Linking CXX executable ../bin/demo_tutorial_sequences_example_conversions_copy -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/tutorial/sequences/example_conversions_copy.cpp.o -o ../bin/demo_tutorial_sequences_example_conversions_copy -lrt -lz -lbz2 +[ 66%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash_next.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 66%] Linking CXX executable ../bin/demo_dox_graph_algorithms_prims_algorithm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_prims_algorithm -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_dox_graph_algorithms_breadth_first_search -make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend +[ 66%] Built target demo_dox_graph_algorithms_prims_algorithm +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend.internal". +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_string_sets_assignment_2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_dox_seeds_seeds_chaining +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_2.cpp +[ 66%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o -o ../bin/demo_tutorial_bed_io_solution3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build -[ 65%] Built target demo_tutorial_sequences_example_conversions_copy -make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend +[ 66%] Built target demo_tutorial_bed_io_solution3 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_final_result +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake --color= -[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend.internal". -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_chaining.cpp -Scanning dependencies of target demo_dox_seeds_seeds_extension +[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/final_result.cpp +[ 66%] Linking CXX executable ../bin/demo_dox_seeds_seeds_chaining +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_chaining.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o -o ../bin/demo_dox_seeds_seeds_chaining -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build +[ 66%] Built target demo_dox_seeds_seeds_chaining +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_extension.cpp -[ 65%] Linking CXX executable ../bin/demo_tutorial_a_first_example_solution_6 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/tutorial/a_first_example/solution_6.cpp.o -o ../bin/demo_tutorial_a_first_example_solution_6 -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_assignment2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_tutorial_a_first_example_solution_6 -make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend.internal". -Scanning dependencies of target demo_dox_graph_algorithms_prims_algorithm +[ 66%] Linking CXX executable ../bin/demo_dox_seeds_seeds_extension +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_extension.dir/link.txt --verbose=1 +[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment2.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o -o ../bin/demo_dox_seeds_seeds_extension -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build +[ 66%] Built target demo_dox_seeds_seeds_extension +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/prims_algorithm.cpp -[ 65%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/tutorial/parsing_command_line_arguments/example1.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example1 -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:34:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, + from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_add_seed.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:34:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89497,23 +89894,106 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 66 | itGapsPattern = begin(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 67 | itGapsEnd = end(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:17:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1838 | oldParentDesc = nodeUp(it); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:10:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89568,6 +90048,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 4, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:10:62: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89591,37 +90087,165 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long long unsigned int>, long long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long long unsigned int>, long long unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String > >; TInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String > >; typename seqan::EnableIf >::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::External > >, seqan::Owner<> >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >; seqan::Iter > >::TSize = long long unsigned int]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:12:43: required from 'void findMUMs(TIndex&, unsigned int) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:72:13: required from 'int runMummy(int, const char**, unsigned int, unsigned int) [with TSpec = seqan::External >]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:149:69: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:443:21: required from 'bool seqan::_skew7ExtendMulti(TTextInput&, const TLimitsString&, TNameInput&, TNameInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TLimitsString = seqan::String > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, long long unsigned int>, long long unsigned int, seqan::File > > > >; TOut0 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 3, int>, long long unsigned int, seqan::File > > > >; TOut3 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long long unsigned int, seqan::File > > > >; TOut5 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 4, seqan::BitPacked<> >, seqan::Tag >, 1, int>, long long unsigned int, seqan::File > > > >; TOut6 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple, 5, seqan::BitPacked<> >, seqan::Tag >, 2, int>, long long unsigned int, seqan::File > > > >; TOut124 = seqan::Pool >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, long long unsigned int>, long long unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:350:34: required from 'bool seqan::Pipe >::process(TInput_&) [with TInput_ = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7_multi.h:294:20: required from 'seqan::Pipe >::Pipe(TInput&, const TLimitsString_&, typename seqan::EnableIf >::Type*) [with TLimitsString_ = seqan::String > >; TInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >, seqan::Caster, seqan::CasterReinterpret> >; TPair_ = seqan::Pair >; TLimitsString = seqan::String > >; typename seqan::EnableIf >::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:107:22: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:461:21: required from 'void seqan::_indexRequireBottomUpIteration(seqan::Index >&) [with TText = seqan::StringSet, seqan::External > >, seqan::Owner<> >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:452:43: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:122:41: required from 'seqan::Iter > >::Iter(TSTree&, seqan::Iter > >::TSize) [with TSTree = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >; seqan::Iter > >::TSize = long long unsigned int]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:12:43: required from 'void findMUMs(TIndex&, unsigned int) [with TIndex = seqan::Index, seqan::External > >, seqan::Owner<> >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:72:13: required from 'int runMummy(int, const char**, unsigned int, unsigned int) [with TSpec = seqan::External >]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:149:69: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89649,6 +90273,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89838,6 +90512,125 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 66%] Linking CXX executable ../bin/demo_dox_arg_parse_argument_parser +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_arg_parse_argument_parser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_arg_parse_argument_parser.dir/dox/arg_parse/argument_parser.cpp.o -o ../bin/demo_dox_arg_parse_argument_parser -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 66%] Built target demo_dox_arg_parse_argument_parser +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alphabets_assignment_1_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 67%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/assignment_1_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -89892,6 +90685,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 68%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90028,6 +90824,18 @@ 82 | inline Triple(Triple const &_p) | ^~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Built target demo_tutorial_string_sets_assignment_2 +make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_iterator +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/iterator.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90136,10 +90944,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 65%] Built target demo_tutorial_parsing_command_line_arguments_example1 -make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90167,8 +90971,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90223,6 +91025,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 68%] Linking CXX executable ../bin/demo_tutorial_graph_graph_hmm +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_hmm.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o -o ../bin/demo_tutorial_graph_graph_hmm -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90277,6 +91082,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Built target demo_tutorial_graph_graph_hmm +make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/DependInfo.cmake --color= +[ 68%] Linking CXX executable ../bin/demo_dox_seeds_seeds_add_seed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/link.txt --verbose=1 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend.internal". +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o -o ../bin/demo_dox_seeds_seeds_add_seed -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash_next.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Scanning dependencies of target demo_tutorial_modifiers_nested +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/nested.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90304,12 +91134,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_dox_index_find_repeats make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/build +[ 68%] Built target demo_dox_seeds_seeds_add_seed +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90365,6 +91194,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend.internal". +[ 68%] Linking CXX executable ../bin/demo_dox_align_profile_profile_seq_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/dox/align_profile/profile_seq_score.cpp.o -o ../bin/demo_dox_align_profile_profile_seq_score -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90392,6 +91226,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90447,16 +91287,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_chaining.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90511,6 +91341,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Built target demo_dox_align_profile_profile_seq_score +make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_parse_lm_stellar +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90565,6 +91406,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 68%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/parse_lm_stellar.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90675,16 +91518,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_extension.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 68%] Linking CXX executable ../bin/demo_tutorial_alphabets_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_alphabets_assignment_1_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Built target demo_tutorial_alphabets_assignment_1_solution +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alphabets_example_bitsPerValue +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_bitsPerValue.cpp +[ 68%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90740,6 +91591,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/tutorial/parsing_command_line_arguments/example1.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: @@ -90795,809 +91647,117 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 65%] Linking CXX executable ../bin/demo_dox_align_profile_profile_seq_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/dox/align_profile/profile_seq_score.cpp.o -o ../bin/demo_dox_align_profile_profile_seq_score -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_dox_align_profile_profile_seq_score -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp -[ 65%] Linking CXX executable ../bin/demo_dox_seeds_seeds_extension -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_extension.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_extension.dir/dox/seeds/seeds_extension.cpp.o -o ../bin/demo_dox_seeds_seeds_extension -lrt -lz -lbz2 -[ 65%] Linking CXX executable ../bin/demo_dox_seeds_seeds_chaining -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_chaining.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_chaining.dir/dox/seeds/seeds_chaining.cpp.o -o ../bin/demo_dox_seeds_seeds_chaining -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_dox_seeds_seeds_extension -make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend.internal". -Scanning dependencies of target demo_dox_seeds_seeds_add_seed -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_add_seed.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_dox_seeds_seeds_chaining -make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend.internal". -Scanning dependencies of target demo_tutorial_graph_graph_hmm -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_hmm.cpp -[ 65%] Linking CXX executable ../bin/demo_dox_arg_parse_argument_parser -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_arg_parse_argument_parser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_arg_parse_argument_parser.dir/dox/arg_parse/argument_parser.cpp.o -o ../bin/demo_dox_arg_parse_argument_parser -lrt -lz -lbz2 -[ 65%] Linking CXX executable ../bin/demo_dox_graph_algorithms_prims_algorithm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/dox/graph_algorithms/prims_algorithm.cpp.o -o ../bin/demo_dox_graph_algorithms_prims_algorithm -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 65%] Built target demo_dox_graph_algorithms_prims_algorithm -make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/depend.internal". -Scanning dependencies of target demo_dox_index_iterator -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Building CXX object demos/CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Built target demo_dox_arg_parse_argument_parser -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alphabets_example_size -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_size.cpp -[ 66%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution3.dir/tutorial/bed_io/solution3.cpp.o -o ../bin/demo_tutorial_bed_io_solution3 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Built target demo_tutorial_bed_io_solution3 -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake --color= -[ 66%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_size -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_size.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_size.dir/tutorial/alphabets/example_size.cpp.o -o ../bin/demo_tutorial_alphabets_example_size -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_dox_index_UNUSED_shape_hash_next -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Building CXX object demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash_next.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Built target demo_tutorial_alphabets_example_size -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_string_sets_assignment_2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/assignment_2.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:34:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:17:32: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/find_repeats.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, - from /build/seqan2-2.4.0+dfsg/demos/dox/seeds/seeds_add_seed.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:34:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:29:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 66%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step4 +[ 68%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape_hash_next +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o -o ../bin/demo_dox_index_UNUSED_shape_hash_next -lrt -lz -lbz2 +[ 68%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step4 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/tutorial/pairwise_sequence_alignment/assignment5_step4.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step4 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 -make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend +[ 68%] Built target demo_dox_index_UNUSED_shape_hash_next +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/DependInfo.cmake --color= -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:17:23: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1838 | oldParentDesc = nodeUp(it); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target demo_tutorial_a_first_example_final_result +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build +[ 68%] Built target demo_tutorial_parsing_command_line_arguments_example1 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend.internal". +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:10:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:10:62: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/final_result.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:15:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/iterator.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 66%] Linking CXX executable ../bin/demo_dox_seeds_seeds_add_seed -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/dox/seeds/seeds_add_seed.cpp.o -o ../bin/demo_dox_seeds_seeds_add_seed -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/UNUSED_shape_hash_next.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 67%] Linking CXX executable ../bin/demo_tutorial_string_sets_assignment_2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/tutorial/string_sets/assignment_2.cpp.o -o ../bin/demo_tutorial_string_sets_assignment_2 -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alphabets_example_ordValue make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 67%] Built target demo_dox_seeds_seeds_add_seed -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend.internal". +[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o +[ 68%] Linking CXX executable ../bin/demo_tutorial_a_first_example_final_result +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_ordValue.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_final_result.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_pattern_matching_assignment2 +Scanning dependencies of target demo_tutorial_sam_and_bam_io_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build -[ 67%] Built target demo_tutorial_string_sets_assignment_2 -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o -o ../bin/demo_tutorial_a_first_example_final_result -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 68%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/DependInfo.cmake --color= -[ 67%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment2.cpp -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/DependInfo.cmake --color= +[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/base.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_assignment2_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 67%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment1.cpp -[ 67%] Linking CXX executable ../bin/demo_dox_index_UNUSED_shape_hash_next -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/dox/index/UNUSED_shape_hash_next.cpp.o -o ../bin/demo_dox_index_UNUSED_shape_hash_next -lrt -lz -lbz2 -[ 67%] Linking CXX executable ../bin/demo_tutorial_graph_graph_hmm -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_hmm.dir/link.txt --verbose=1 +[ 69%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment2_solution.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_hmm.dir/tutorial/graph/graph_hmm.cpp.o -o ../bin/demo_tutorial_graph_graph_hmm -lrt -lz -lbz2 -[ 67%] Built target demo_dox_index_UNUSED_shape_hash_next -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend +[ 69%] Built target demo_tutorial_a_first_example_final_result +make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alphabets_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend.internal". +[ 69%] Linking CXX executable ../bin/demo_dox_index_iterator +Scanning dependencies of target demo_tutorial_basics_allocator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_iterator.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/assignment_1_solution.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o -o ../bin/demo_dox_index_iterator -lrt -lz -lbz2 +[ 70%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/allocator.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_graph_graph_hmm -make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend +[ 70%] Built target demo_dox_index_iterator +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/iterator.cpp -[ 68%] Linking CXX executable ../bin/demo_dox_index_iterator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_iterator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_iterator.dir/dox/index/iterator.cpp.o -o ../bin/demo_dox_index_iterator -lrt -lz -lbz2 -[ 68%] Linking CXX executable ../bin/demo_tutorial_alphabets_assignment_1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/tutorial/alphabets/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_alphabets_assignment_1_solution -lrt -lz -lbz2 +[ 70%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp +[ 70%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment2 -lrt -lz -lbz2 +[ 70%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_bitsPerValue +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o -o ../bin/demo_tutorial_alphabets_example_bitsPerValue -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_dox_index_iterator -make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend +[ 70%] Built target demo_tutorial_pattern_matching_assignment2 +make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_alphabets_assignment_1_solution -Scanning dependencies of target demo_tutorial_modifiers_nested +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/DependInfo.cmake --color= -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend.internal". -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/nested.cpp -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 +Scanning dependencies of target demo_dox_score_score make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build +make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp -[ 68%] Linking CXX executable ../bin/demo_tutorial_a_first_example_final_result -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_final_result.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_final_result.dir/tutorial/a_first_example/final_result.cpp.o -o ../bin/demo_tutorial_a_first_example_final_result -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_a_first_example_final_result -make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend +[ 70%] Built target demo_tutorial_alphabets_example_bitsPerValue +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_parse_lm_stellar +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/DependInfo.cmake --color= +[ 72%] Building CXX object demos/CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/score/score.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_assignment1_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/parse_lm_stellar.cpp +[ 72%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment1_solution.cpp +[ 72%] Linking CXX executable ../bin/demo_unassigned_or_unused_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_iterator.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -91625,6 +91785,21 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o -o ../bin/demo_unassigned_or_unused_iterator -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 72%] Built target demo_unassigned_or_unused_iterator +make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/depend.internal". +[ 72%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_ordValue +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o -o ../bin/demo_tutorial_alphabets_example_ordValue -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_basics_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -91653,6 +91828,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 72%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/base.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 72%] Built target demo_tutorial_alphabets_example_ordValue +make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment1.cpp:2: @@ -91672,86 +91856,76 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 68%] Linking CXX executable ../bin/demo_unassigned_or_unused_iterator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_iterator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_iterator.dir/unassigned_or_unused/iterator.cpp.o -o ../bin/demo_unassigned_or_unused_iterator -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_unassigned_or_unused_iterator -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alphabets_example_bitsPerValue +Scanning dependencies of target demo_tutorial_basics_show_alphabets make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build +make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_bitsPerValue.cpp -[ 68%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/tutorial/pattern_matching/assignment2.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment2 -lrt -lz -lbz2 -[ 68%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_bitsPerValue -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/tutorial/alphabets/example_bitsPerValue.cpp.o -o ../bin/demo_tutorial_alphabets_example_bitsPerValue -lrt -lz -lbz2 +[ 72%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/show_alphabets.cpp +[ 72%] Linking CXX executable ../bin/demo_tutorial_basics_allocator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_allocator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o -o ../bin/demo_tutorial_basics_allocator -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_pattern_matching_assignment2 -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend +[ 72%] Built target demo_tutorial_basics_allocator +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sam_and_bam_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_index_bidirectional_search make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/base.cpp +[ 72%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp +[ 72%] Linking CXX executable ../bin/demo_tutorial_modifiers_nested +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_nested.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o -o ../bin/demo_tutorial_modifiers_nested -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_alphabets_example_bitsPerValue -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend +[ 72%] Built target demo_tutorial_modifiers_nested +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alphabets_example_ordValue +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Building CXX object demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alphabets/example_ordValue.cpp -[ 68%] Linking CXX executable ../bin/demo_tutorial_modifiers_nested -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_nested.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_nested.dir/tutorial/modifiers/nested.cpp.o -o ../bin/demo_tutorial_modifiers_nested -lrt -lz -lbz2 +[ 72%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp +[ 72%] Linking CXX executable ../bin/demo_tutorial_basics_show_alphabets +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_show_alphabets.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o -o ../bin/demo_tutorial_basics_show_alphabets -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 68%] Built target demo_tutorial_modifiers_nested -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend +[ 72%] Built target demo_tutorial_basics_show_alphabets +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pattern_matching_assignment2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend.internal". +[ 72%] Linking CXX executable ../bin/demo_tutorial_basics_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o -o ../bin/demo_tutorial_basics_base -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_bed_io_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build -[ 68%] Linking CXX executable ../bin/demo_tutorial_alphabets_example_ordValue -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/link.txt --verbose=1 +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/tutorial/alphabets/example_ordValue.cpp.o -o ../bin/demo_tutorial_alphabets_example_ordValue -lrt -lz -lbz2 -[ 69%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment2_solution.cpp +[ 73%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 69%] Built target demo_tutorial_alphabets_example_ordValue -make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend +[ 73%] Built target demo_tutorial_basics_base +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend.internal". -Scanning dependencies of target demo_tutorial_basics_allocator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend.internal". +Scanning dependencies of target demo_tutorial_consensus_alignment_without_positions make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 70%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/allocator.cpp +[ 74%] Building CXX object demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/parse_lm_stellar.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -91822,16 +91996,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 70%] Linking CXX executable ../bin/demo_tutorial_basics_allocator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_allocator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_allocator.dir/tutorial/basics/allocator.cpp.o -o ../bin/demo_tutorial_basics_allocator -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 70%] Built target demo_tutorial_basics_allocator -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/base.cpp:2: @@ -91857,7 +92030,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/base.cpp:2: @@ -91884,11 +92056,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 70%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, @@ -91910,95 +92077,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 72%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment1 -lrt -lz -lbz2 -[ 72%] Linking CXX executable ../bin/demo_dox_index_find_repeats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_find_repeats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o -o ../bin/demo_dox_index_find_repeats -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 72%] Built target demo_tutorial_simple_rna_seq_genequant_assignment1 -make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/depend -[ 72%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment6_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/tutorial/parsing_command_line_arguments/assignment6_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment6_solution -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/depend.internal". -Scanning dependencies of target demo_dox_score_score -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object demos/CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/score/score.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Built target demo_dox_index_find_repeats -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pattern_matching_assignment1_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment1_solution.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Built target demo_tutorial_parsing_command_line_arguments_assignment6_solution -make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_basics_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/base.cpp -[ 73%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment2_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment2_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Built target demo_tutorial_pattern_matching_assignment2_solution -make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend.internal". -Scanning dependencies of target demo_tutorial_basics_show_alphabets -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/show_alphabets.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 73%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_base -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Built target demo_tutorial_sam_and_bam_io_base -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_bidirectional_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 73%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]': @@ -92121,58 +92199,197 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 74%] Linking CXX executable ../bin/demo_unassigned_or_unused_parse_lm_stellar -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o -o ../bin/demo_unassigned_or_unused_parse_lm_stellar -lrt -lz -lbz2 -[ 74%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step2 -lrt -lz -lbz2 +[ 74%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/tutorial/pattern_matching/assignment2_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment2_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 74%] Built target demo_unassigned_or_unused_parse_lm_stellar -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend +[ 74%] Built target demo_tutorial_pattern_matching_assignment2_solution +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pattern_matching_assignment1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 74%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp +[ 74%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:9:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:9:85: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 75%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/tutorial/simple_rna_seq/genequant_assignment1.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 74%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 -[ 74%] Linking CXX executable ../bin/demo_tutorial_basics_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_base.dir/link.txt --verbose=1 -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend -[ 74%] Linking CXX executable ../bin/demo_tutorial_basics_show_alphabets -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_show_alphabets.dir/link.txt --verbose=1 +[ 75%] Built target demo_tutorial_simple_rna_seq_genequant_assignment1 +make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_base.dir/tutorial/basics/base.cpp.o -o ../bin/demo_tutorial_basics_base -lrt -lz -lbz2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_show_alphabets.dir/tutorial/basics/show_alphabets.cpp.o -o ../bin/demo_tutorial_basics_show_alphabets -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_bed_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_iterators_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build +make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_base.dir/tutorial/iterators/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_base.dir/tutorial/iterators/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/base.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] + 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 70 | operator=(HistoryStackFM_ const & _origin) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +[ 75%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/tutorial/sam_and_bam_io/base.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_base -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 75%] Built target demo_tutorial_basics_show_alphabets -[ 75%] Built target demo_tutorial_basics_base -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend +[ 75%] Built target demo_tutorial_sam_and_bam_io_base +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_file_io_overview_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend.internal". +[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp +[ 75%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: @@ -92199,17 +92416,63 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_tutorial_pattern_matching_assignment1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build +[ 75%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_consensus_alignment_without_positions +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 70 | operator=(HistoryStackFM_ const & _origin) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' + 70 | operator=(HistoryStackFM_ const & _origin) + | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment1.cpp -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: @@ -92318,7 +92581,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp +[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp +[ 75%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment1_solution -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: @@ -92400,6 +92667,46 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 75%] Built target demo_tutorial_pattern_matching_assignment1_solution +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_file_io_overview_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::FMIndex >; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:115:27: required from 'seqan::Iter >, seqan::VSTree > > >::Iter(seqan::Iter >, seqan::VSTree > > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:13:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 534 | *cb->cur = pool.undefinedValue; + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: @@ -92535,538 +92842,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 762 | *cur = Val_; - | ~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 311 | buffer[pool.handlerArgs(Val_)] = Val_; - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 517 | *cb.cur = item; - | ~~~~~~~~^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:9:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:9:85: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/bed_io/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/tutorial/pattern_matching/assignment1_solution.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment1_solution -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_pattern_matching_assignment1_solution -make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_iterators_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_base.dir/tutorial/iterators/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_base.dir/tutorial/iterators/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/base.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h: In instantiation of 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1342:26: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] - 1342 | TTargetValue temp_copy(std::forward(_value)); //temp copy because resize could invalidate _value - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 70 | operator=(HistoryStackFM_ const & _origin) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:21:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 70 | operator=(HistoryStackFM_ const & _origin) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::HistoryStackFM_ >*; TParam = seqan::HistoryStackFM_ >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String >, seqan::Alloc<> >; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::HistoryStackFM_ >; TTargetSpec = seqan::Alloc<>; TValue = seqan::HistoryStackFM_ >&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String >, seqan::Alloc<> >&; TSource = seqan::HistoryStackFM_ >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:494:16: required from 'void seqan::_historyPush(seqan::Iter >, seqan::VSTree > > >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bifm_stree.h:92:17: required from 'bool seqan::_goDownString(seqan::Iter > >, seqan::VSTree > >&, const TString&, TSize&, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig; TSpec = seqan::ParentLinks<>; TString = seqan::String, seqan::Alloc<> >; TSize = unsigned int; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:271:25: required from 'bool seqan::_goDownObject(seqan::Iter >, seqan::VSTree > >&, const TObject&, seqan::True, TDirection) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; TDirection = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:300:25: required from 'bool seqan::goDown(seqan::Iter >, seqan::VSTree > >&, const TObject&, const Fwd&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::ParentLinks<>; TObject = seqan::String, seqan::Alloc<> >; seqan::Fwd = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:17:38: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::HistoryStackFM_ >::HistoryStackFM_(const seqan::HistoryStackFM_ >&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:172, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:70:5: note: because 'seqan::HistoryStackFM_ >' has user-provided 'const seqan::HistoryStackFM_& seqan::HistoryStackFM_::operator=(const seqan::HistoryStackFM_&) [with TSize = unsigned int; TAlphabet = seqan::SimpleType]' - 70 | operator=(HistoryStackFM_ const & _origin) - | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_dox_score_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_score_score.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o -o ../bin/demo_dox_score_score -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::end() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:633:42: required from 'void seqan::Handler, seqan::Tag >::end() [with THandler1 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:904:28: required from 'bool seqan::Pool::endWrite() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:786:13: required from 'seqan::Pool::~Pool() [with TValue = seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:243:12: required from 'void seqan::_createSuffixArrayPipelining(TSA&, const TObject&, TAlgSpec) [with TSA = seqan::String > >; TObject = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:186:37: required from 'void seqan::_createSuffixArrayWrapper(TSA&, const TText&, const TAlgSpec&, seqan::False) [with TSA = seqan::String > >; TText = seqan::String, seqan::Alloc<> >; TAlgSpec = seqan::Skew7]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:198:34: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::FMIndex >; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TOccSpec = void; TIndexSpec = seqan::FastFMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index, seqan::Alloc<> >, seqan::FMIndex > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_bidirectional_stree.h:115:27: required from 'seqan::Iter >, seqan::VSTree > > >::Iter(seqan::Iter >, seqan::VSTree > > >::TBiIndex&) [with TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex >; TSpec = seqan::Preorder; seqan::Iter >, seqan::VSTree > > >::TBiIndex = seqan::Index, seqan::Alloc<> >, seqan::BidirectionalIndex > > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:13:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:534:34: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >& seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 534 | *cb->cur = pool.undefinedValue; - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93202,8 +92977,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 76%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender7.h:163:29: required from 'bool seqan::_skew7Extend(TTextInput&, TNameInput&, TOut0&, TOut3&, TOut5&, TOut6&, TOut124&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TOut3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TOut6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TOut124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:362:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:312:20: [ skipping 6 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93258,10 +93085,88 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/unassigned_or_unused/tutorials_custim_io/parse_gff2.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 -lrt -lz -lbz2 -[ 76%] Built target demo_dox_score_score -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:123:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: required from 'seqan::Pipe::Pipe(TInput&) [with TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew7.h:376:49: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:762:18: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 762 | *cur = Val_; + | ~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:447:21: required from 'void seqan::Pipe, seqan::Merger7Multi >::insertStream(unsigned int) [with TInput0 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec >, seqan::Tuple, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >; TLimitsString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:465:13: [ skipping 7 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >& seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93289,10 +93194,60 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler::push(const TValue&) [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::Handler::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:622:44: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 311 | buffer[pool.handlerArgs(Val_)] = Val_; + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'void seqan::Handler >, seqan::MapperAsyncWriter>::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:623:43: required from 'void seqan::Handler, seqan::Tag >::push(const TValue&) [with THandler1 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::MapperMemAdapter>; THandler2 = seqan::Handler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::MapperAsyncWriter>; seqan::Handler, seqan::Tag >::TValue = seqan::Triple, seqan::Tuple, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:881:25: required from 'void seqan::Pool::push(const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:1167:16: required from 'void seqan::push(seqan::Pool&, const TValue&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pump_extender3.h:101:17: required from 'bool seqan::_skew3Extend(TTextInput&, TNameInput&, TOut0&, TOut12&) [with TTextInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TNameInput = seqan::Pool >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >; TOut0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TOut12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:269:29: required from 'bool seqan::Pipe::process(TInput_&) [with TInput_ = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >; TInput = seqan::Pipe >, seqan::MapperSpec >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Filter >, unsigned int> > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:218:20: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:517:21: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 517 | *cb.cur = item; + | ~~~~~~~~^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93347,10 +93302,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_tutorial_file_io_overview_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 75%] Linking CXX executable ../bin/demo_dox_index_find_repeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_find_repeats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_find_repeats.dir/dox/index/find_repeats.cpp.o -o ../bin/demo_dox_index_find_repeats -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93406,21 +93360,129 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 10 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp -[ 76%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend +[ 75%] Built target demo_dox_index_find_repeats +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sam_and_bam_io_example1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 13 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:614:26: required from 'bool seqan::indexCreate(seqan::Index&, FibreSA, TSpecAlg) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TSpecAlg = seqan::Skew7; seqan::FibreSA = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:658:27: required from 'bool seqan::indexCreate(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::StringSet > >; TSpec = seqan::IndexEsa<>; TFibre = seqan::FibreSA_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:453:21: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::StringSet > >; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:15:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +[ 75%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_bidirectional_search.cpp:2: @@ -93476,38 +93538,64 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_iterators_base +[ 75%] Linking CXX executable ../bin/demo_tutorial_iterators_base cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_base.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_base.dir/tutorial/iterators/base.cpp.o -o ../bin/demo_tutorial_iterators_base -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_iterators_base -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend +[ 75%] Built target demo_tutorial_iterators_base +make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_file_io_overview_solution2 -[ 76%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend.internal". +Scanning dependencies of target demo_dox_modifier_cyclic_shape_snippets make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/link.txt --verbose=1 +make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment1 -lrt -lz -lbz2 -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp +[ 75%] Building CXX object demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp +[ 76%] Linking CXX executable ../bin/demo_unassigned_or_unused_parse_lm_stellar +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/unassigned_or_unused/parse_lm_stellar.cpp.o -o ../bin/demo_unassigned_or_unused_parse_lm_stellar -lrt -lz -lbz2 +[ 76%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/tutorial/pairwise_sequence_alignment/assignment5_step2.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_pattern_matching_assignment1 -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend +[ 76%] Built target demo_unassigned_or_unused_parse_lm_stellar +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sam_and_bam_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build +[ 76%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend.internal". +Scanning dependencies of target demo_tutorial_file_io_overview_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp +Scanning dependencies of target demo_tutorial_fragment_store_access_aligned_reads +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp +[ 76%] Linking CXX executable ../bin/demo_dox_score_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_score_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_score_score.dir/dox/score/score.cpp.o -o ../bin/demo_dox_score_score -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_dox_score_score +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -93519,6 +93607,147 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp +[ 76%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/tutorial/pattern_matching/assignment1.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_pattern_matching_assignment1 +make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend.internal". +Scanning dependencies of target demo_tutorial_alignment_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_align.dir/tutorial/alignment/align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_align.dir/tutorial/alignment/align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp +[ 76%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment6_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/tutorial/parsing_command_line_arguments/assignment6_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment6_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_parsing_command_line_arguments_assignment6_solution +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend.internal". +Scanning dependencies of target demo_tutorial_genome_annotations_assignment_1_hint +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:386:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::Iterator::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:58:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' + 203 | CyclicShape(CyclicShape const & other) : + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::FixedShape<2, seqan::GappedShape >, 1>; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape >, 1> > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:32:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'constexpr seqan::CyclicShape >, 1> >& seqan::CyclicShape >, 1> >::operator=(const seqan::CyclicShape >, 1> >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:288:5: note: because 'seqan::CyclicShape >, 1> >' has user-provided 'seqan::CyclicShape >, RightOffset> >::CyclicShape(const seqan::CyclicShape >, RightOffset> >&) [with unsigned int LeftOffset = 2; unsigned int RightOffset = 1; int P00 = 1; int P01 = 1; int P02 = 3; int P03 = 2; int P04 = 0; int P05 = 0; int P06 = 0; int P07 = 0; int P08 = 0; int P09 = 0; int P10 = 0; int P11 = 0; int P12 = 0; int P13 = 0; int P14 = 0; int P15 = 0; int P16 = 0; int P17 = 0; int P18 = 0; int P19 = 0]' + 288 | CyclicShape(CyclicShape const &) + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::FixedShape<2, seqan::GappedShape >, 1>; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, 1> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape >, 1> >; typename seqan::Size > >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape >, 1> > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:32:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'constexpr seqan::CyclicShape >, 1> >& seqan::CyclicShape >, 1> >::operator=(const seqan::CyclicShape >, 1> >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:288:5: note: because 'seqan::CyclicShape >, 1> >' has user-provided 'seqan::CyclicShape >, RightOffset> >::CyclicShape(const seqan::CyclicShape >, RightOffset> >&) [with unsigned int LeftOffset = 2; unsigned int RightOffset = 1; int P00 = 1; int P01 = 1; int P02 = 3; int P03 = 2; int P04 = 0; int P05 = 0; int P06 = 0; int P07 = 0; int P08 = 0; int P09 = 0; int P10 = 0; int P11 = 0; int P12 = 0; int P13 = 0; int P14 = 0; int P15 = 0; int P16 = 0; int P17 = 0; int P18 = 0; int P19 = 0]' + 288 | CyclicShape(CyclicShape const &) + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:51:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' + 203 | CyclicShape(CyclicShape const & other) : + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape > >; typename seqan::Size > >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' +/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:51:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] + 452 | cargo(me) = cargo(_origin); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' + 203 | CyclicShape(CyclicShape const & other) : + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp:3: @@ -93539,6 +93768,31 @@ 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, @@ -93568,8 +93822,9 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -93590,18 +93845,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, @@ -93609,13 +93866,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp:3: @@ -93683,27 +93933,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -93732,6 +93961,67 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 76%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o -o ../bin/demo_tutorial_bed_io_solution1 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_bed_io_solution1 +make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/realign.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/consensus_aligner_interface.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:68, @@ -93751,6 +94041,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +Scanning dependencies of target demo_dox_statistics_load_markov_model +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 76%] Building CXX object demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -93829,6 +94146,84 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/shape_onegapped.h:107:9: note: because 'seqan::Shape, seqan::OneGappedShape>' has user-provided 'seqan::Shape::Shape(const seqan::Shape&) [with TValue = seqan::SimpleType]' 107 | Shape(Shape const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 76%] Linking CXX executable ../bin/demo_dox_modifier_cyclic_shape_snippets +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o -o ../bin/demo_dox_modifier_cyclic_shape_snippets -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_dox_modifier_cyclic_shape_snippets +make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -93850,6 +94245,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:55, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, @@ -93872,6 +94271,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_fragment_store_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:105, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp:3: @@ -93892,6 +94295,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -94299,31 +94704,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp:3: @@ -94406,10 +94786,9 @@ | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -94419,14 +94798,14 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -94523,31 +94902,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: note: synthesized method 'seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >& seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Dependent > >, seqan::IndexQGram, seqan::OneGappedShape>, seqan::Tag > >&)' first required here 110 | target = source; | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, @@ -94608,30 +94962,32 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_bed_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_bed_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_bed_io_solution1.dir/tutorial/bed_io/solution1.cpp.o -o ../bin/demo_tutorial_bed_io_solution1 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution2.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/consensus_alignment/without_positions.cpp:3: @@ -94663,36 +95019,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -94706,7 +95036,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/example1.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -94741,6 +95071,96 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = const seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:138:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 138 | it = begin(row1); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:139:21: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 139 | itEnd = end(row1); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = unsigned int; TValue2 = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:110:79: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1562 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1575 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1598 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter > seqan::operator-(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]': /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:382:27: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, TDPCell&, TDPCell&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TDPCell = seqan::DPCell_ >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' /build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:453:18: required from 'void seqan::_computeTrack(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSeqHValue&, const TSeqVValue&, const TSeqVIterator&, const TSeqVIterator&, const TScoringScheme&, const TColumnDescriptor&, const TDPProfile&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSeqHValue = seqan::ConsensusScoreSequenceEntry >, seqan::Alloc<> > >; TSeqVValue = seqan::ConsensusScoreSequenceEntry, seqan::Alloc<> >, seqan::InfixSegment> >; TSeqVIterator = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AdaptorIterator*, seqan::Tag > >; TScoringScheme = seqan::Score >, seqan::Score > > >; TColumnDescriptor = seqan::MetaColumnDescriptor, seqan::Tag >; TDPProfile = seqan::DPProfile_ >, seqan::Tag, seqan::TracebackOn, seqan::Tag > >, seqan::Tag >]' @@ -94770,213 +95190,41 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_bed_io_solution1 -make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend.internal". -Scanning dependencies of target demo_dox_modifier_cyclic_shape_snippets -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:132, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h: In function 'void seqan::_lcpProcessMulti(TTextInput&, const TLimitsString&, TInvertedSAInput&, TDest&, seqan::LcpConfig) [with TTextInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >; TLimitsString = seqan::String > >; TInvertedSAInput = seqan::Pool >, 2, void>, void>, seqan::MapperSpec >, 2, void>, void>, seqan::String > >, long long unsigned int>, long long unsigned int, seqan::File > > > >; TDest = seqan::Pool, seqan::MapperSpec, long long unsigned int>, long long unsigned int, seqan::File > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::host' may be used uninitialized in this function [-Wmaybe-uninitialized] - 87 | class Iter > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::objNo' may be used uninitialized in this function [-Wmaybe-uninitialized] -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::host' may be used uninitialized in this function [-Wmaybe-uninitialized] - 87 | class Iter > - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::objNo' may be used uninitialized in this function [-Wmaybe-uninitialized] -[ 76%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution3 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_solution3 -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_file_io_overview_solution3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp -[ 76%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:386:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::Iterator::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:58:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' - 203 | CyclicShape(CyclicShape const & other) : - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::FixedShape<2, seqan::GappedShape >, 1>; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape >, 1> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape >, 1> > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:32:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'constexpr seqan::CyclicShape >, 1> >& seqan::CyclicShape >, 1> >::operator=(const seqan::CyclicShape >, 1> >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:288:5: note: because 'seqan::CyclicShape >, 1> >' has user-provided 'seqan::CyclicShape >, RightOffset> >::CyclicShape(const seqan::CyclicShape >, RightOffset> >&) [with unsigned int LeftOffset = 2; unsigned int RightOffset = 1; int P00 = 1; int P01 = 1; int P02 = 3; int P03 = 2; int P04 = 0; int P05 = 0; int P06 = 0; int P07 = 0; int P08 = 0; int P09 = 0; int P10 = 0; int P11 = 0; int P12 = 0; int P13 = 0; int P14 = 0; int P15 = 0; int P16 = 0; int P17 = 0; int P18 = 0; int P19 = 0]' - 288 | CyclicShape(CyclicShape const &) - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, 1> > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::FixedShape<2, seqan::GappedShape >, 1>; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, 1> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape >, 1> >; typename seqan::Size > >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape >, 1> > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape >, 1> > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:32:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'constexpr seqan::CyclicShape >, 1> >& seqan::CyclicShape >, 1> >::operator=(const seqan::CyclicShape >, 1> >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:288:5: note: because 'seqan::CyclicShape >, 1> >' has user-provided 'seqan::CyclicShape >, RightOffset> >::CyclicShape(const seqan::CyclicShape >, RightOffset> >&) [with unsigned int LeftOffset = 2; unsigned int RightOffset = 1; int P00 = 1; int P01 = 1; int P02 = 3; int P03 = 2; int P04 = 0; int P05 = 0; int P06 = 0; int P07 = 0; int P08 = 0; int P09 = 0; int P10 = 0; int P11 = 0; int P12 = 0; int P13 = 0; int P14 = 0; int P15 = 0; int P16 = 0; int P17 = 0; int P18 = 0; int P19 = 0]' - 288 | CyclicShape(CyclicShape const &) - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:371:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::begin(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Rooted_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::ModifiedIterator >, seqan::AdaptorIterator > >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:51:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' - 203 | CyclicShape(CyclicShape const & other) : - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h: In instantiation of 'void seqan::_copyCargoImpl(TDest&, TSource&, seqan::True) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:458:19: required from 'void seqan::_copyCargo(TDest&, TSource&) [with TDest = seqan::ModifiedIterator > > > >; TSource = const seqan::ModifiedString >, seqan::ModCyclicShape > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:427:15: required from 'typename seqan::Iterator > >, const seqan::Tag >::Type seqan::end(const seqan::ModifiedString > >&, seqan::Tag) [with THost = seqan::String >; TSpec = seqan::GappedShape >; TTagSpec = seqan::Standard_; typename seqan::Iterator > >, const seqan::Tag >::Type = seqan::ModifiedIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_cyclic_shape.h:689:15: required from 'typename seqan::Size > >::Type seqan::length(const seqan::ModifiedString >&) [with THost = seqan::String >; TSpec = seqan::CyclicShape > >; typename seqan::Size > >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1086:31: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::ModifiedString >, seqan::ModCyclicShape > > > >; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:801:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::ModifiedString&) [with TStream = std::basic_ostream; THost = seqan::String >; TSpec = seqan::ModCyclicShape > > >]' -/build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:51:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_string.h:452:15: warning: implicitly-declared 'seqan::CyclicShape > >& seqan::CyclicShape > >::operator=(const seqan::CyclicShape > >&)' is deprecated [-Wdeprecated-copy] - 452 | cargo(me) = cargo(_origin); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:68, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/dox/modifier/cyclic_shape_snippets.cpp:9: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/cyclic_shape.h:203:5: note: because 'seqan::CyclicShape > >' has user-provided 'seqan::CyclicShape > >::CyclicShape(const seqan::CyclicShape > >&)' - 203 | CyclicShape(CyclicShape const & other) : - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend.internal". -Scanning dependencies of target demo_tutorial_fragment_store_access_aligned_reads -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp -[ 76%] Linking CXX executable ../bin/demo_dox_modifier_cyclic_shape_snippets -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/dox/modifier/cyclic_shape_snippets.cpp.o -o ../bin/demo_dox_modifier_cyclic_shape_snippets -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_dox_modifier_cyclic_shape_snippets -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution4 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:36:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -94984,48 +95232,27 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -95034,14 +95261,14 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -95050,32 +95277,32 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:36:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -95088,7 +95315,7 @@ | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -95098,14 +95325,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -95122,77 +95347,49 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 76%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/tutorial/pairwise_sequence_alignment/alignment_global_standard.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard +make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend.internal". +Scanning dependencies of target demo_tutorial_generic_programming_template_subclassing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/generic_programming/template_subclassing.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' @@ -95215,55 +95412,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = unsigned int; TValue2 = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:110:79: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1562 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1575:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1575 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1598:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1598 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -95274,7 +95425,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ @@ -95293,8 +95444,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' @@ -95318,37 +95469,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' @@ -95360,20 +95484,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' /build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' @@ -95385,13 +95509,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here /build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ @@ -95400,37 +95524,36 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:36:60: required from here + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -95438,15 +95561,14 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -95455,51 +95577,58 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:36:60: required from here + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:11:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 76%] Linking CXX executable ../bin/demo_tutorial_generic_programming_template_subclassing In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' @@ -95510,195 +95639,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 773 | Iter > > result = lhs; | ^~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/link.txt --verbose=1 /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] 775 | return result; | ^~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution4.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_file_io_overview_solution1 -make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend.internal". -Scanning dependencies of target demo_tutorial_alignment_align -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_alignment_align.dir/tutorial/alignment/align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_alignment_align.dir/tutorial/alignment/align.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp -[ 76%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_bidirectional_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o -o ../bin/demo_tutorial_index_iterators_index_bidirectional_search -lrt -lz -lbz2 -[ 76%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/link.txt --verbose=1 -[ 76%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example1 -lrt -lz -lbz2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_sam_and_bam_io_example1 -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend.internal". -[ 76%] Built target demo_tutorial_index_iterators_index_bidirectional_search -make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend.internal". -Scanning dependencies of target demo_tutorial_genome_annotations_assignment_1_hint -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp -Scanning dependencies of target demo_dox_statistics_load_markov_model -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_file_io_overview_solution2 -make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_fragment_store_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/base.cpp -/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:138:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 138 | it = begin(row1); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:139:21: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 139 | itEnd = end(row1); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/alignment/align.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution1 -lrt -lz -lbz2 -[ 76%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution3 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_index_iterators_iterator_solution1 -make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_file_io_overview_solution3 -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend.internal". -Scanning dependencies of target demo_tutorial_generic_programming_template_subclassing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend.internal". -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/generic_programming/template_subclassing.cpp -Scanning dependencies of target demo_tutorial_iterators_assignment_3_workshop -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/tutorial/iterators/assignment_3_workshop.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/tutorial/iterators/assignment_3_workshop.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o -o ../bin/demo_tutorial_generic_programming_template_subclassing -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -95718,47 +95678,33 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:11:39: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1035:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const CharString&, bool) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = void; TFSConfig = seqan::FragmentStoreConfig; TFileNames = char*]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:16:48: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:3: + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -95785,6 +95731,76 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_generic_programming_template_subclassing +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:18:28: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/access_aligned_reads.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/load_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Scanning dependencies of target demo_tutorial_iterators_assignment_3_workshop +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_hint.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -95802,26 +95818,24 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_generic_programming_template_subclassing -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/link.txt --verbose=1 +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/tutorial/iterators/assignment_3_workshop.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/tutorial/iterators/assignment_3_workshop.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop.cpp [ 76%] Linking CXX executable ../bin/demo_tutorial_alignment_align cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_alignment_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/tutorial/generic_programming/template_subclassing.cpp.o -o ../bin/demo_tutorial_generic_programming_template_subclassing -lrt -lz -lbz2 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_alignment_align.dir/tutorial/alignment/align.cpp.o -o ../bin/demo_tutorial_alignment_align -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_generic_programming_template_subclassing +[ 76%] Built target demo_tutorial_alignment_align make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/depend.internal". -[ 76%] Built target demo_tutorial_alignment_align -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment4_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend.internal". +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment4_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -95849,12 +95863,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment4_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment4_solution.cpp +[ 76%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/tutorial/simple_rna_seq/genequant_solution3.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -95883,9 +95894,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_sequence_io_solution4 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, from /build/seqan2-2.4.0+dfsg/demos/tutorial/fragment_store/base.cpp:2: @@ -95905,6 +95913,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_solution3 +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequence_io_solution4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/tutorial/sequence_io/solution4.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution4.dir/tutorial/sequence_io/solution4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution4.cpp @@ -95998,6 +96016,38 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/tutorial/genome_annotations/assignment_2_solution.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/tutorial/genome_annotations/assignment_2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_2_solution.cpp +[ 76%] Linking CXX executable ../bin/demo_dox_statistics_load_markov_model +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_statistics_load_markov_model.dir/link.txt --verbose=1 +[ 76%] Linking CXX executable ../bin/demo_tutorial_fragment_store_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o -o ../bin/demo_dox_statistics_load_markov_model -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o -o ../bin/demo_tutorial_fragment_store_base -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_dox_statistics_load_markov_model +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/DependInfo.cmake --color= +[ 76%] Built target demo_tutorial_fragment_store_base +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_modifiers_assignment1_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/tutorial/modifiers/assignment1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/tutorial/modifiers/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/assignment1_solution.cpp +Scanning dependencies of target demo_unassigned_or_unused_index_node_predicate +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_node_predicate.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution4.cpp:1: @@ -96215,38 +96265,45 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_fragment_store_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_base.dir/tutorial/fragment_store/base.cpp.o -o ../bin/demo_tutorial_fragment_store_base -lrt -lz -lbz2 -[ 76%] Linking CXX executable ../bin/demo_dox_statistics_load_markov_model -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_statistics_load_markov_model.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_statistics_load_markov_model.dir/dox/statistics/load_markov_model.cpp.o -o ../bin/demo_dox_statistics_load_markov_model -lrt -lz -lbz2 +[ 76%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_1_hint +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_1_hint -lrt -lz -lbz2 +[ 76%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/tutorial/file_io_overview/solution1.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_fragment_store_base -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend +[ 76%] Built target demo_tutorial_genome_annotations_assignment_1_hint +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_index_node_predicate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build +[ 76%] Built target demo_tutorial_file_io_overview_solution1 +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_node_predicate.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake --color= +[ 76%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/link.txt --verbose=1 +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment3 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_dox_statistics_load_markov_model -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/tutorial/sam_and_bam_io/example1.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_example1 -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_modifiers_assignment1_solution +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment2_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build +[ 76%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/link.txt --verbose=1 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/tutorial/modifiers/assignment1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/tutorial/modifiers/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/assignment1_solution.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/tutorial/file_io_overview/solution2.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution2 -lrt -lz -lbz2 +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment2_solution.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_2_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -96269,6 +96326,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 76%] Built target demo_tutorial_sam_and_bam_io_example1 +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_file_io_overview_solution2 +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_genome_annotations_assignment_3_solution In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_2_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': @@ -96291,6 +96362,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp +Scanning dependencies of target demo_tutorial_genome_annotations_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_2_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -96357,19 +96439,35 @@ [ 76%] Linking CXX executable ../bin/demo_tutorial_modifiers_assignment1_solution cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/tutorial/modifiers/assignment1_solution.cpp.o -o ../bin/demo_tutorial_modifiers_assignment1_solution -lrt -lz -lbz2 +[ 76%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_bidirectional_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/tutorial/index_iterators/index_bidirectional_search.cpp.o -o ../bin/demo_tutorial_index_iterators_index_bidirectional_search -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 76%] Built target demo_tutorial_modifiers_assignment1_solution -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_assignment3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_gff_and_gtf_io_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp +[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/base.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_index_iterators_index_bidirectional_search +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_gff_and_gtf_io_example1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/index_node_predicate.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -96443,70 +96541,156 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_1_hint -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/tutorial/genome_annotations/assignment_1_hint.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_1_hint -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_genome_annotations_assignment_1_hint -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment2_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Linking CXX executable ../bin/demo_tutorial_fragment_store_access_aligned_reads -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/link.txt --verbose=1 -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment2_solution.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o -o ../bin/demo_tutorial_fragment_store_access_aligned_reads -lrt -lz -lbz2 -[ 76%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_node_predicate -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o -o ../bin/demo_unassigned_or_unused_index_node_predicate -lrt -lz -lbz2 +[ 77%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/tutorial/file_io_overview/solution3.cpp.o -o ../bin/demo_tutorial_file_io_overview_solution3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_unassigned_or_unused_index_node_predicate -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend +[ 77%] Built target demo_tutorial_file_io_overview_solution3 +make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_genome_annotations_assignment_3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_graph_solution_1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/solution_1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 77%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_base -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_fragment_store_access_aligned_reads -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend +[ 77%] Built target demo_tutorial_gff_and_gtf_io_base +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake --color= -[ 76%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution4 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_genome_annotations_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_gff_and_gtf_io_example2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example2.cpp +[ 77%] Linking CXX executable ../bin/demo_unassigned_or_unused_index_node_predicate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/unassigned_or_unused/index_node_predicate.cpp.o -o ../bin/demo_unassigned_or_unused_index_node_predicate -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_solution4 -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend +[ 77%] Built target demo_unassigned_or_unused_index_node_predicate +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_gff_and_gtf_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_file_io_overview_example1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/base.cpp +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/example1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeRight(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:34:27: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:876:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 876 | Iter > tmp(it); + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:878:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 878 | return tmp; + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::createSibling(seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:60:27: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:1071:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 1071 | Iter > siblingIter(it); + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:1073:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 1073 | return siblingIter; + | ^~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -96566,10 +96750,9 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -96578,14 +96761,14 @@ | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -96595,12 +96778,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:36:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -96617,158 +96800,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 76%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/tutorial/gff_and_gtf_io/base.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_base -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_gff_and_gtf_io_base -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_gff_and_gtf_io_example1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeRight(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:34:27: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:876:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 876 | Iter > tmp(it); - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:878:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 878 | return tmp; - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::createSibling(seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:60:27: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:1071:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 1071 | Iter > siblingIter(it); - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:1073:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 1073 | return siblingIter; - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:19:39: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -96785,62 +96827,53 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:132, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/mummy.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h: In function 'void seqan::_lcpProcessMulti(TTextInput&, const TLimitsString&, TInvertedSAInput&, TDest&, seqan::LcpConfig) [with TTextInput = seqan::Pipe, seqan::External > >, seqan::Owner<> > >, seqan::Source<> >; TLimitsString = seqan::String > >; TInvertedSAInput = seqan::Pool >, 2, void>, void>, seqan::MapperSpec >, 2, void>, void>, seqan::String > >, long long unsigned int>, long long unsigned int, seqan::File > > > >; TDest = seqan::Pool, seqan::MapperSpec, long long unsigned int>, long long unsigned int, seqan::File > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::host' may be used uninitialized in this function [-Wmaybe-uninitialized] + 87 | class Iter > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::objNo' may be used uninitialized in this function [-Wmaybe-uninitialized] +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::host' may be used uninitialized in this function [-Wmaybe-uninitialized] + 87 | class Iter > + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/iter_concat_virtual.h:87:7: warning: '.seqan::Iter, seqan::External > >, seqan::Owner<> >, seqan::ConcatVirtual<> >::objNo' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:19:39: required from here + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:36:60: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/base.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:11:39: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -96884,29 +96917,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -96937,9 +96966,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:11:39: required from here @@ -96977,143 +97005,145 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 77%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution4.dir/tutorial/sequence_io/solution4.cpp.o -o ../bin/demo_tutorial_sequence_io_solution4 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:11:39: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_sequence_io_solution4 -make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:12:36: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_3_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_graph_solution_1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/solution_1.cpp -[ 77%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_2_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/tutorial/genome_annotations/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_2_solution -lrt -lz -lbz2 -[ 77%] Linking CXX executable ../bin/demo_tutorial_graph_solution_1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_solution_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o -o ../bin/demo_tutorial_graph_solution_1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_graph_solution_1 -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_gff_and_gtf_io_example2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example2.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_genome_annotations_assignment_2_solution -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_file_io_overview_example1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/example1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_assignment3.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/example2.cpp:2: @@ -97186,6 +97216,48 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 77%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/tutorial/index_iterators/iterator_solution1.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Built target demo_tutorial_index_iterators_iterator_solution1 +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_gff_and_gtf_io_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution1.cpp +[ 77%] Linking CXX executable ../bin/demo_tutorial_graph_solution_1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_solution_1.dir/link.txt --verbose=1 +[ 77%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_solution_1.dir/tutorial/graph/solution_1.cpp.o -o ../bin/demo_tutorial_graph_solution_1 -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution4.dir/tutorial/sequence_io/solution4.cpp.o -o ../bin/demo_tutorial_sequence_io_solution4 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Built target demo_tutorial_graph_solution_1 +make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend.internal". +Scanning dependencies of target demo_howto_using_zip_iterator +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Built target demo_tutorial_sequence_io_solution4 +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend +[ 77%] Building CXX object demos/CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/using_zip_iterator.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/example1.cpp:2: @@ -97211,6 +97283,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_tutorial_index_iterators_index_search +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/file_io_overview/example1.cpp:2: @@ -97258,41 +97336,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 77%] Linking CXX executable ../bin/demo_dox_index_mummy -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_mummy.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_mummy.dir/dox/index/mummy.cpp.o -o ../bin/demo_dox_index_mummy -lrt -lz -lbz2 -[ 77%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_example1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_gff_and_gtf_io_example1 -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_gff_and_gtf_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution1.cpp -[ 77%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_3_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_3_solution -lrt -lz -lbz2 +[ 77%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/tutorial/genome_annotations/assignment_2_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_2_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_genome_annotations_assignment_3_solution -make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend +[ 77%] Built target demo_tutorial_genome_annotations_assignment_2_solution +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend.internal". -Scanning dependencies of target demo_howto_using_zip_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_gff_and_gtf_io_solution2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/using_zip_iterator.cpp +[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution1.cpp:1: @@ -97365,46 +97424,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 77%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/tutorial/gff_and_gtf_io/example1.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_example1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_dox_index_mummy -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_search -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search.cpp -[ 77%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o -o ../bin/demo_tutorial_genome_annotations_base -lrt -lz -lbz2 -[ 77%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment4_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment4_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_genome_annotations_base -[ 77%] Linking CXX executable ../bin/demo_howto_using_zip_iterator -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_using_zip_iterator.dir/link.txt --verbose=1 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o -o ../bin/demo_howto_using_zip_iterator -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_gff_and_gtf_io_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Building CXX object demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp -[ 77%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_example2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_example2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_howto_using_zip_iterator +[ 77%] Built target demo_tutorial_gff_and_gtf_io_example1 make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/DependInfo.cmake --color= @@ -97416,24 +97440,110 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 77%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp +[ 77%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/tutorial/simple_rna_seq/genequant_solution4.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution4 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_parsing_command_line_arguments_assignment4_solution +[ 77%] Built target demo_tutorial_simple_rna_seq_genequant_solution4 make -f demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/depend.internal". +Scanning dependencies of target demo_tutorial_graph_graph_dijkstra make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_gff_and_gtf_io_example2 +make -f demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_dijkstra.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 78%] Linking CXX executable ../bin/demo_howto_using_zip_iterator +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_using_zip_iterator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_using_zip_iterator.dir/howto/using_zip_iterator.cpp.o -o ../bin/demo_howto_using_zip_iterator -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 78%] Built target demo_howto_using_zip_iterator make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_graph_graph_dijkstra +Scanning dependencies of target demo_tutorial_index_iterators_index_assignment1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -97443,14 +97553,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_dijkstra.cpp -Scanning dependencies of target demo_tutorial_index_iterators_index_assignment1 +[ 78%] Linking CXX executable ../bin/demo_tutorial_fragment_store_access_aligned_reads +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/tutorial/fragment_store/access_aligned_reads.cpp.o -o ../bin/demo_tutorial_fragment_store_access_aligned_reads -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build +[ 78%] Built target demo_tutorial_fragment_store_access_aligned_reads +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_index_assignment2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': @@ -97573,97 +97691,73 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 78%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/link.txt --verbose=1 -[ 78%] Linking CXX executable ../bin/demo_tutorial_consensus_alignment_without_positions -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment3 -lrt -lz -lbz2 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o -o ../bin/demo_tutorial_consensus_alignment_without_positions -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:13:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/gff_and_gtf_io/solution2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +[ 78%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_example2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/tutorial/gff_and_gtf_io/example2.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_example2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Built target demo_tutorial_simple_rna_seq_genequant_assignment3 -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend +[ 78%] Built target demo_tutorial_gff_and_gtf_io_example2 +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution3 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp +[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp +[ 78%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/tutorial/genome_annotations/assignment_3_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_3_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 78%] Built target demo_tutorial_genome_annotations_assignment_3_solution +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_index_preorder +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/tutorial/index_iterators/index_preorder.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/tutorial/index_iterators/index_preorder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp +[ 79%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_unassigned_or_unused_tutorial_file_io_mmap_string_example +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend.internal". +Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution5 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp +[ 79%] Linking CXX executable ../../bin/test_sequence_v2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequence_v2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_sequence_v2.dir/test_sequence_v2.cpp.o -o ../../bin/test_sequence_v2 -lrt -lz -lbz2 +[ 79%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_search +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_search.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o -o ../bin/demo_tutorial_index_iterators_index_search -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_index_iterators_index_search +make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend.internal". +Scanning dependencies of target demo_dox_index_shape_hash_init +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/shape_hash_init.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -97673,19 +97767,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Built target demo_tutorial_consensus_alignment_without_positions -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::ParentLinks; TDfsOrder = seqan::Postorder_]': @@ -97700,6 +97781,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +[ 79%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment4_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -97718,6 +97801,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/tutorial/parsing_command_line_arguments/assignment4_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment4_solution -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > > >; TSpec = seqan::Preorder]': @@ -97825,38 +97909,216 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 78%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/unassigned_or_unused/tutorial_file_io/mmap_string_example.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example -lrt -lz -lbz2 -[ 78%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_search -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_search.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_search.dir/tutorial/index_iterators/index_search.cpp.o -o ../bin/demo_tutorial_index_iterators_index_search -lrt -lz -lbz2 +[ 79%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_base.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Built target demo_unassigned_or_unused_tutorial_file_io_mmap_string_example -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_base.dir/tutorial/genome_annotations/base.cpp.o -o ../bin/demo_tutorial_genome_annotations_base -lrt -lz -lbz2 +[ 79%] Built target demo_tutorial_parsing_command_line_arguments_assignment4_solution +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_preorder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build +[ 79%] Built target test_sequence_v2 +make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/tutorial/index_iterators/index_preorder.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/tutorial/index_iterators/index_preorder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake --color= +Scanning dependencies of target demo_tutorial_index_iterators_index_search2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_index_iterators_index_search -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/depend.internal". make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend.internal". -Scanning dependencies of target demo_tutorial_simple_rna_seq_genequant_solution5 +[ 79%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/link.txt --verbose=1 +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search2.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution1 -lrt -lz -lbz2 +Scanning dependencies of target demo_dox_find_finder_index make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build +make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_genome_annotations_base +make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_gff_and_gtf_io_solution1 +make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend.internal". +Scanning dependencies of target demo_dox_align_profile_profile_seq_frac_score +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_frac_score.cpp +Scanning dependencies of target demo_tutorial_indices_find2_index_approx +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Postorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:109:41: required from 'seqan::Iter > >::Iter(TSTree&) [with TSTree = seqan::Index > > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:18:54: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::ParentLinks<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:19:20: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1838 | oldParentDesc = nodeUp(it); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +[ 79%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution2 -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:14:63: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -97864,8 +98126,229 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:14:63: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_gff_and_gtf_io_solution2 +make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend.internal". +Scanning dependencies of target demo_dox_align_compute_alignment_stats +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/compute_alignment_stats.cpp +[ 79%] Linking CXX executable ../bin/demo_tutorial_graph_graph_dijkstra +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o -o ../bin/demo_tutorial_graph_graph_dijkstra -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_graph_graph_dijkstra +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_iterator_assignment2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:17:82: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:17:82: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 351 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2256:24: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:22:11: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1838 | oldParentDesc = nodeUp(it); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:22:11: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: @@ -98270,24 +98753,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: @@ -98370,22 +98835,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > > >; TSpec = seqan::BottomUp<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1605:14: required from 'void seqan::goBegin(seqan::Iter >, seqan::VSTree > >&) [with TText = seqan::StringSet > >; TIndexSpec = void; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:453:20: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > > >; TSpec = seqan::Postorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_algs_multi.h:109:41: required from 'seqan::Iter > >::Iter(TSTree&) [with TSTree = seqan::Index > > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:18:54: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: @@ -98440,61 +98889,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:22:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment1.cpp:3: @@ -98605,133 +98999,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::ParentLinks<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:19:20: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1838 | oldParentDesc = nodeUp(it); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:14:63: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::IndexEsa<> >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:14:63: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:18:19: required from 'void constrainedDFS() [with TIndexSpec = seqan::IndexEsa<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:34:33: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 79%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/tutorial/gff_and_gtf_io/solution1.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_gff_and_gtf_io_solution1 -make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend.internal". -[ 79%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment2_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment2_solution -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: @@ -98759,12 +99026,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_dox_index_shape_hash_init -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/index/shape_hash_init.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/dox/index/shape_hash_init.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: @@ -99143,6 +99413,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeDown(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]': +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:146:38: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 853 | Iter > tmp(it); + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 855 | return tmp; + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: @@ -99225,15 +99511,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple >, seqan::Tuple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = seqan::Pair >; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: @@ -99343,6 +99620,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = unsigned int; TValue2 = int]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:109:79: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1562 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: @@ -99384,212 +99688,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -[ 79%] Linking CXX executable ../bin/demo_tutorial_graph_graph_dijkstra -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/tutorial/graph/graph_dijkstra.cpp.o -o ../bin/demo_tutorial_graph_graph_dijkstra -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:17:82: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:17:82: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 351 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'bool seqan::_goDown(seqan::Iter >, seqan::VSTree > >&, seqan::VSTreeIteratorTraits) [with TText = seqan::String >; TIndexSpec = void; TSpec = seqan::ParentLinks<>; TDfsOrder = seqan::Preorder_]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1880:20: required from 'bool seqan::goDown(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::ParentLinks<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2256:24: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:22:11: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1838:27: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1838 | oldParentDesc = nodeUp(it); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2259:22: required from 'void seqan::goNextImpl(seqan::Iter > > >&, seqan::VSTreeIteratorTraits) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder; THideEmptyEdges = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1660:19: required from 'void seqan::goNext(seqan::Iter >&, TTraits) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >; TTraits = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1655:15: required from 'void seqan::goNext(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:268:11: required from 'const seqan::Iter& seqan::operator++(seqan::Iter&) [with TContainer = seqan::Index > >; TSpec = seqan::VSTree > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:22:11: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::String >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:351:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(const T&, Rooted) [with T = seqan::Segment >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:392:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(const T&, seqan::Tag) [with T = seqan::Segment >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/iter_stream.h:515:17: required from 'typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type seqan::directionIterator(TContainer&, const TDirection&) [with TContainer = const seqan::Segment >, seqan::InfixSegment>; TDirection = seqan::Tag; typename seqan::DisableIf >, typename seqan::Iterator >::Type>::Type = seqan::Iter >, seqan::InfixSegment>, seqan::AdaptorIterator > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:87: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:21:47: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_preorder.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_parsing_command_line_arguments_assignment2_solution -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_index_search2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search2.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_graph_graph_dijkstra -make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/depend.internal". -Scanning dependencies of target demo_dox_find_finder_index -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeDown(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]': -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:146:38: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 853 | Iter > tmp(it); - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 855 | return tmp; - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = const seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TVertexDescriptor&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TVertexDescriptor = unsigned int; TValue = int; TCargo = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1532:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = int; TCargo = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1513:18: required from 'void seqan::findIntervals(seqan::String&, const seqan::IntervalTree&, TValue2, TValue2) [with TValue = int; TCargo = unsigned int; TValue2 = int]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:109:79: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1562:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1562 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, @@ -99604,6 +99702,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_assignment2.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, @@ -99618,9 +99730,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ -[ 79%] Linking CXX executable ../bin/demo_tutorial_gff_and_gtf_io_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/tutorial/gff_and_gtf_io/solution2.cpp.o -o ../bin/demo_tutorial_gff_and_gtf_io_solution2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -99648,142 +99757,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_gff_and_gtf_io_solution2 -make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend.internal". -[ 79%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o -o ../bin/demo_tutorial_file_io_overview_example1 -lrt -lz -lbz2 -Scanning dependencies of target demo_dox_align_profile_profile_seq_frac_score -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/link.txt --verbose=1 -[ 79%] Building CXX object demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_frac_score.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:36:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution3 -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_file_io_overview_example1 -make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend.internal". -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:36:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -Scanning dependencies of target demo_tutorial_indices_find2_index_approx -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp +[ 79%] Linking CXX executable ../bin/demo_dox_index_shape_hash_init +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_shape_hash_init.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o -o ../bin/demo_dox_index_shape_hash_init -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/index/shape_hash_init.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -99792,8 +99770,20 @@ 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_dox_index_shape_hash_init +make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_vcf_io_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search2.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -99801,44 +99791,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 79%] Built target demo_tutorial_index_iterators_iterator_solution3 -make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend.internal". -Scanning dependencies of target demo_dox_align_compute_alignment_stats -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -[ 79%] Building CXX object demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/compute_alignment_stats.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/index_search2.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': @@ -99902,94 +99854,6 @@ [ 79%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_preorder cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/tutorial/index_iterators/index_preorder.cpp.o -o ../bin/demo_tutorial_index_iterators_index_preorder -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_index_iterators_index_preorder -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_iterator_assignment2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Linking CXX executable ../bin/demo_dox_index_shape_hash_init -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_shape_hash_init.dir/link.txt --verbose=1 -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_shape_hash_init.dir/dox/index/shape_hash_init.cpp.o -o ../bin/demo_dox_index_shape_hash_init -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_dox_index_shape_hash_init -make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_vcf_io_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/vcf_io/base.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:220, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h: In instantiation of 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [2]]': @@ -100033,6 +99897,36 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:36:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 79%] Linking CXX executable ../bin/demo_tutorial_file_io_overview_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_file_io_overview_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_file_io_overview_example1.dir/tutorial/file_io_overview/example1.cpp.o -o ../bin/demo_tutorial_file_io_overview_example1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:171, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h: In instantiation of 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [2]; seqan::FinderSTree = const seqan::Tag]': @@ -100088,6 +99982,195 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = const seqan::CompressedSA >, void, seqan::FMIndexConfig >]' 105 | Iter(Iter const & other_) : | ^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_index_iterators_index_preorder +make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_dox_statistics_build_markov_model +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Building CXX object demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 79%] Built target demo_tutorial_file_io_overview_example1 +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:36:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution2.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 343 | return TIterator(me, begin(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 478 | return TIterator(me, end(me, Standard())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' + 116 | Iter(typename Parameter_::Type container_, TIterator it_) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100115,8 +100198,55 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 79%] Linking CXX executable ../bin/demo_tutorial_vcf_io_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_base.dir/link.txt --verbose=1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100225,7 +100355,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o -o ../bin/demo_tutorial_vcf_io_base -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100253,15 +100382,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 80%] Linking CXX executable ../bin/demo_tutorial_vcf_io_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_vcf_io_base.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100316,6 +100438,58 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_vcf_io_base.dir/tutorial/vcf_io/base.cpp.o -o ../bin/demo_tutorial_vcf_io_base -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:169:26: required from 'seqan::Gaps >::Gaps(const TGapAnchors&) [with TSource = seqan::Tag; TGapAnchors = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:36, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: required from 'seqan::Holder >::Holder(const THostValue&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; seqan::Holder >::THostValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:180:26: required from 'seqan::Gaps >::Gaps(const TSourceNoConstNoRef&, TGapAnchors&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; seqan::Gaps >::TSourceNoConstNoRef = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:31:37: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:37, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/simple_rna_seq/genequant_solution5.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100343,10 +100517,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_search2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/link.txt --verbose=1 -[ 79%] Built target demo_tutorial_vcf_io_base +[ 80%] Built target demo_tutorial_vcf_io_base +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_indexed_fasta_io_solution1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100366,6 +100543,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:311:44: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] 311 | buffer[pool.handlerArgs(Val_)] = Val_; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -100374,6 +100552,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: @@ -100401,243 +100580,43 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o -o ../bin/demo_tutorial_index_iterators_index_search2 -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend.internal". -Scanning dependencies of target demo_dox_statistics_build_markov_model -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Building CXX object demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::EmptyEdges]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:407:59: required from 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [2]; seqan::FinderSTree = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [2]]' -/build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:12:28: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 343 | return TIterator(me, begin(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h: In instantiation of 'typename seqan::Iterator >::Type seqan::_endDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:512:23: required from 'typename seqan::Iterator >::Type seqan::end(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:497:15: required from 'typename seqan::Iterator::Type>::Type seqan::end(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:478:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 478 | return TIterator(me, end(me, Standard())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' - 116 | Iter(typename Parameter_::Type container_, TIterator it_) - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::EmptyEdges]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:407:59: required from 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [2]; seqan::FinderSTree = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [2]]' -/build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:12:28: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 202 | *refNext = *I; - | ~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 203 | *I = *refPrev; - | ~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] - 243 | *cur = *refPrev; - | ~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, - from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' - 82 | inline Triple(Triple const &_p) - | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_index_iterators_index_search2 -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_index_iterators_iterator_solution2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution2.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:343:12: required from 'typename seqan::Iterator >::Type seqan::_beginDefault(T&, Rooted) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >; seqan::Rooted = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:385:25: required from 'typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type seqan::begin(T&, seqan::Tag) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; TSpec = seqan::Rooted_; typename seqan::DisableIf::Type> >, typename seqan::Iterator >::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:362:17: required from 'typename seqan::Iterator::Type>::Type seqan::begin(T&) [with T = seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>, seqan::AdaptorIterator, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::CountingIteratorImpl_ > >, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:21:9: required from 'main():: [with auto:4 = seqan::Iter, seqan::Alloc<> >, seqan::BidirectionalIndex > >, seqan::VSTree > >; seqan::DnaString = seqan::String, seqan::Alloc<> >; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:509:17: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, uint32_t, uint32_t, uint8_t, const seqan::OptimalSearch&, uint8_t, const TDir&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDir = seqan::Tag; TDistanceTag = seqan::Tag; uint32_t = unsigned int; uint8_t = unsigned char]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:556:25: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const seqan::OptimalSearch&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:571:29: required from 'void seqan::_optimalSearchScheme(TDelegate&, seqan::Iter >, seqan::VSTree > >, const TNeedle&, const std::array, N>&, const TDistanceTag&) [with TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndex = seqan::FMIndex<>; TIndexSpec = seqan::Preorder; TNeedle = seqan::String, seqan::Alloc<> >; unsigned int nbrBlocks = 4; unsigned int N = 3; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find2_index_approx.h:592:25: required from 'void seqan::find(TDelegate&, seqan::Index >&, const seqan::String&, const TDistanceTag&) [with unsigned int minErrors = 0; unsigned int maxErrors = 2; TDelegate = main()::; TText = seqan::String, seqan::Alloc<> >; TIndexSpec = seqan::FMIndex<>; TChar = seqan::SimpleType; TStringSpec = seqan::Alloc<>; TDistanceTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:29:59: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, void, seqan::FMIndexConfig >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::CompressedSA, seqan::Alloc<> >, void, seqan::FMIndexConfig >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ +[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:10:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 1731 | it._parentDesc = value(it); + | ~~~~~~~~~~~~~~~^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:10:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] + 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' + 222 | VertexEsa(VertexEsa const &other): + | ^~~~~~~~~ +[ 80%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/tutorial/index_iterators/iterator_solution3.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -100665,6 +100644,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_frac_score.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Built target demo_tutorial_index_iterators_iterator_solution3 +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_assignment_3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_3.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -100800,15 +100804,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -100863,6 +100858,61 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple >, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple >, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:302:21: required from 'void seqan::Pipe, seqan::Merger7>::insertStream(unsigned int) [with TInput0 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 3, int>, unsigned int, seqan::File > > > >; TInput3 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput5 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 1, int>, unsigned int, seqan::File > > > >; TInput6 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::SorterSpec, seqan::Tuple >, seqan::Tag >, 2, int>, unsigned int, seqan::File > > > >; TInput124 = seqan::Pool, seqan::Tuple >, seqan::Tag >, seqan::MapperSpec, seqan::Tuple >, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger7.h:320:13: [ skipping 8 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::EmptyEdges]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:407:59: required from 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [2]; seqan::FinderSTree = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [2]]' +/build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:12:28: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple >, seqan::Tag >& seqan::Triple, seqan::Tuple >, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple >, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -100890,18 +100940,74 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/include/seqan/align_profile.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/align_profile/profile_seq_frac_score.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 80%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/tutorial/parsing_command_line_arguments/assignment2_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment2_solution -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h: In instantiation of 'seqan::Buffer& seqan::processBuffer(seqan::Buffer >&, seqan::BufferHandler >, seqan::Tag >&) [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TConfig = seqan::MapperConfigSize, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > >; typename TConfig::File = seqan::File >]': +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:332:33: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer& seqan::BufferHandler, seqan::Tag >::next() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:556:50: required from 'seqan::BufferHandler, seqan::Tag >::TBuffer seqan::BufferHandler, seqan::Tag >::next() [with TBufferHandler1 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; TBufferHandler2 = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >; seqan::BufferHandler, seqan::Tag >::TBuffer = seqan::Buffer, seqan::Tuple, seqan::Tag >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pipe_base.h:744:38: required from 'void seqan::Handler::pop() [with TBufferHandler = seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag >, seqan::BufferHandler, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >, seqan::Tag > >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_base.h:870:24: required from 'seqan::Pool& seqan::Pool::operator++() [with TValue = seqan::Triple, seqan::Tuple, seqan::Tag >; TSpec = seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/pipe_merger3.h:111:17: required from 'seqan::Pipe, seqan::Merger3>& seqan::Pipe, seqan::Merger3>::operator++() [with TInput0 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::SorterSpec, seqan::Tuple, seqan::Tag >, int>, unsigned int, seqan::File > > > >; TInput12 = seqan::Pool, seqan::Tuple, seqan::Tag >, seqan::MapperSpec, seqan::Tuple, seqan::Tag >, unsigned int>, unsigned int, seqan::File > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_skew3.h:329:13: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_shims.h:726:27: required from 'bool seqan::indexRequire(seqan::Index&, seqan::Tag) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TFibre = seqan::FibreSALF_]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm_stree.h:183:17: required from 'void seqan::_indexRequireTopDownIteration(seqan::Index >&) [with TText = seqan::String >; TOccSpec = void; TIndexSpec = seqan::FMIndexConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:211:42: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index >, seqan::FMIndex<> >; TSpec = seqan::EmptyEdges]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_fm.h:407:59: required from 'void seqan::_findFirstIndex(seqan::Finder >, TSpecFinder>&, const TPattern&, FinderSTree) [with TText = seqan::String >; TSpec = void; TConfig = seqan::FMIndexConfig; TSpecFinder = const seqan::Tag; TPattern = char [2]; seqan::FinderSTree = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String >; TSpec = seqan::FMIndex<>; TSpecFinder = const seqan::Tag; TPattern = char [2]]' +/build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:12:28: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:202:30: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 202 | *refNext = *I; + | ~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:203:24: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 203 | *I = *refPrev; + | ~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/pipe/pool_mapper.h:243:26: warning: implicitly-declared 'constexpr seqan::Triple, seqan::Tuple, seqan::Tag >& seqan::Triple, seqan::Tuple, seqan::Tag >::operator=(const seqan::Triple, seqan::Tuple, seqan::Tag >&)' is deprecated [-Wdeprecated-copy] + 243 | *cur = *refPrev; + | ~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_aggregate.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, + from /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_index.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' + 82 | inline Triple(Triple const &_p) + | ^~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Built target demo_tutorial_parsing_command_line_arguments_assignment2_solution +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_genome_annotations_assignment_1_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -100956,6 +101062,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp +[ 81%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_assignment3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/tutorial/simple_rna_seq/genequant_assignment3.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_assignment3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -101011,21 +101123,16 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1491:22: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:10:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1731:24: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 1731 | it._parentDesc = value(it); - | ~~~~~~~~~~~~~~~^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ +[ 81%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_search2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/tutorial/index_iterators/index_search2.cpp.o -o ../bin/demo_tutorial_index_iterators_index_search2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Built target demo_tutorial_simple_rna_seq_genequant_assignment3 +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/find2_index_approx.cpp:5: @@ -101081,22 +101188,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2236:15: required from 'void seqan::clear(seqan::Iter >&) [with TIndex = seqan::Index > >; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:1492:14: required from 'void seqan::goRoot(seqan::Iter, seqan::VSTree >&) [with TText = seqan::String >; TIndexSpec = seqan::IndexEsa<>; TSpec = seqan::TopDown<>]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:212:19: required from 'seqan::Iter > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:349:25: required from 'seqan::Iter > > >::Iter(TIndex&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:10:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h:2230:19: warning: implicitly-declared 'constexpr seqan::VertexEsa& seqan::VertexEsa::operator=(const seqan::VertexEsa&)' is deprecated [-Wdeprecated-copy] - 2230 | value(it) = typename VertexDescriptor::Type(MinimalCtor()); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_assignment2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' - 222 | VertexEsa(VertexEsa const &other): - | ^~~~~~~~~ +Scanning dependencies of target demo_tutorial_indices_assignment_1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Built target demo_tutorial_index_iterators_index_search2 +make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/DependInfo.cmake --color= +[ 81%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/tutorial/indices/assignment_1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_assignment_1.dir/tutorial/indices/assignment_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_1.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend.internal". +Scanning dependencies of target demo_dox_align_global_alignment_banded +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Building CXX object demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_banded.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -101179,6 +101289,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[ 81%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_assignment2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Built target demo_tutorial_index_iterators_iterator_assignment2 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend.internal". +Scanning dependencies of target demo_tutorial_a_first_example_example_tags_for_print +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/example_tags_for_print.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -101210,6 +101336,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:222:9: note: because 'seqan::VertexEsa' has user-provided 'seqan::VertexEsa::VertexEsa(const seqan::VertexEsa&) [with TSize = unsigned int]' 222 | VertexEsa(VertexEsa const &other): | ^~~~~~~~~ +[ 82%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o -o ../bin/demo_tutorial_sequences_assignment_3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -101228,33 +101357,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:138, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution2.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_stree.h: In instantiation of 'void seqan::_historyClear(seqan::Iter > >&) [with TIndex = seqan::Index > >; TSpec = seqan::Preorder]': @@ -101312,33 +101414,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Built target demo_tutorial_sequences_assignment_3 +make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, from /build/seqan2-2.4.0+dfsg/demos/tutorial/index_iterators/iterator_solution2.cpp:2: @@ -101359,11 +101441,55 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_indices_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp +[ 82%] Linking CXX executable ../bin/demo_dox_align_compute_alignment_stats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_compute_alignment_stats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o -o ../bin/demo_dox_align_compute_alignment_stats -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Built target demo_dox_align_compute_alignment_stats +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_example1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/example1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -101374,30 +101500,37 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_1.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -101416,8 +101549,7 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -101429,8 +101561,7 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -101439,9 +101570,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here @@ -101467,12 +101597,12 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -101495,8 +101625,8 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' @@ -101518,89 +101648,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 80%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/tutorial/index_iterators/iterator_assignment2.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_assignment2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Built target demo_tutorial_index_iterators_iterator_assignment2 -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake --color= -[ 80%] Linking CXX executable ../bin/demo_dox_align_compute_alignment_stats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_compute_alignment_stats.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_compute_alignment_stats.dir/dox/align/compute_alignment_stats.cpp.o -o ../bin/demo_dox_align_compute_alignment_stats -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_indexed_fasta_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Built target demo_dox_align_compute_alignment_stats -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequences_assignment_3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/assignment_3.cpp -[ 80%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Built target demo_tutorial_index_iterators_iterator_solution2 -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_genome_annotations_assignment_1_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Building CXX object demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp -[ 81%] Linking CXX executable ../bin/demo_dox_align_profile_profile_seq_frac_score -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o -o ../bin/demo_dox_align_profile_profile_seq_frac_score -lrt -lz -lbz2 -[ 81%] Linking CXX executable ../bin/demo_tutorial_sequences_assignment_3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_assignment_3.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_assignment_3.dir/tutorial/sequences/assignment_3.cpp.o -o ../bin/demo_tutorial_sequences_assignment_3 -lrt -lz -lbz2 -[ 81%] Built target demo_dox_align_profile_profile_seq_frac_score -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_indices_assignment_1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/tutorial/indices/assignment_1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_assignment_1.dir/tutorial/indices/assignment_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Built target demo_tutorial_sequences_assignment_3 -make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend.internal". -Scanning dependencies of target demo_dox_align_global_alignment_banded -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Building CXX object demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/align/global_alignment_banded.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -101610,45 +101659,20 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:3: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -101660,17 +101684,18 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indexed_fasta_io/solution1.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:10:39: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -101687,24 +101712,30 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:10:39: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:2: + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -101732,6 +101763,34 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/genome_annotations/assignment_1_solution.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' @@ -101771,47 +101830,117 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_1.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 81%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_solution1 -lrt -lz -lbz2 -[ 81%] Linking CXX executable ../bin/demo_tutorial_indices_assignment_1 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:18:41: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, + from /build/seqan2-2.4.0+dfsg/demos/dox/statistics/build_markov_model.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 82%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tags_for_print +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o -o ../bin/demo_tutorial_a_first_example_example_tags_for_print -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 82%] Built target demo_tutorial_a_first_example_example_tags_for_print +make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend.internal". +Scanning dependencies of target demo_dox_misc_enumerate_strings +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 83%] Building CXX object demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/enumerate_strings.cpp +[ 83%] Linking CXX executable ../bin/demo_tutorial_index_iterators_iterator_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/tutorial/index_iterators/iterator_solution2.cpp.o -o ../bin/demo_tutorial_index_iterators_iterator_solution2 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 83%] Built target demo_tutorial_index_iterators_iterator_solution2 +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_iterators_assignment_1_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 83%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_1_solution.cpp +[ 83%] Linking CXX executable ../bin/demo_dox_align_profile_profile_seq_frac_score +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/dox/align_profile/profile_seq_frac_score.cpp.o -o ../bin/demo_dox_align_profile_profile_seq_frac_score -lrt -lz -lbz2 +[ 83%] Linking CXX executable ../bin/demo_tutorial_indices_assignment_1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_assignment_1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_assignment_1.dir/tutorial/indices/assignment_1.cpp.o -o ../bin/demo_tutorial_indices_assignment_1 -lrt -lz -lbz2 +[ 83%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_example1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 83%] Built target demo_dox_align_profile_profile_seq_frac_score +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Built target demo_tutorial_indexed_fasta_io_solution1 -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend -[ 81%] Built target demo_tutorial_indices_assignment_1 -make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/depend +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend.internal". +[ 83%] Built target demo_tutorial_indices_assignment_1 +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_sequence_io_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build +[ 83%] Built target demo_unassigned_or_unused_tutorials_custim_io_example1 +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_example_tags_for_print +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake --color= +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 83%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution1.cpp +Scanning dependencies of target demo_tutorial_indices_assignment_2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend.internal". make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Scanning dependencies of target demo_tutorial_indices_base -[ 82%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/example_tags_for_print.cpp +Scanning dependencies of target demo_tutorial_iterators_assignment_3_workshop_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 82%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop_solution.cpp +[ 84%] Linking CXX executable ../bin/demo_tutorial_consensus_alignment_without_positions +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/tutorial/consensus_alignment/without_positions.cpp.o -o ../bin/demo_tutorial_consensus_alignment_without_positions -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': @@ -101821,25 +101950,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 82%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o -o ../bin/demo_tutorial_index_iterators_index_assignment1 -lrt -lz -lbz2 -[ 82%] Linking CXX executable ../bin/demo_tutorial_a_first_example_example_tags_for_print -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/tutorial/a_first_example/example_tags_for_print.cpp.o -o ../bin/demo_tutorial_a_first_example_example_tags_for_print -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 82%] Built target demo_tutorial_a_first_example_example_tags_for_print -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend +[ 84%] Built target demo_tutorial_consensus_alignment_without_positions +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorials_custim_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_banded make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 82%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorials_custim_io/example1.cpp +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_banded.cpp +[ 84%] Linking CXX executable ../bin/demo_tutorial_indexed_fasta_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/tutorial/indexed_fasta_io/solution1.cpp.o -o ../bin/demo_tutorial_indexed_fasta_io_solution1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -101862,18 +101988,34 @@ 429 | Index(Index const &other): | ^~~~~ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 82%] Built target demo_tutorial_index_iterators_index_assignment1 -make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend +[ 84%] Built target demo_tutorial_indexed_fasta_io_solution1 +make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend.internal". -Scanning dependencies of target demo_dox_misc_enumerate_strings +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend.internal". +Scanning dependencies of target demo_howto_align_gaps_clipping make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build +make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Building CXX object demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/misc/enumerate_strings.cpp +[ 84%] Building CXX object demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/align_gaps_clipping.cpp +[ 84%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_1_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_tutorial_iterators_assignment_1_solution +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_iterators_assignment_4_workshop_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_4_workshop_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -101922,6 +102064,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 84%] Linking CXX executable ../bin/demo_dox_misc_enumerate_strings +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_enumerate_strings.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o -o ../bin/demo_dox_misc_enumerate_strings -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102022,7 +102167,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 83%] Linking CXX executable ../bin/demo_dox_align_global_alignment_banded In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102048,8 +102192,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_global_alignment_banded.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o -o ../bin/demo_dox_align_global_alignment_banded -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_dox_misc_enumerate_strings +make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102150,6 +102295,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102175,6 +102322,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend.internal". +Scanning dependencies of target demo_tutorial_iterators_sequence_iterator_demo +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102227,6 +102380,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/sequence_iterator_demo.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102331,13 +102486,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Built target demo_dox_align_global_alignment_banded -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102390,10 +102538,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -Scanning dependencies of target demo_tutorial_iterators_assignment_1_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102446,8 +102590,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 83%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_1_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102500,6 +102642,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +[ 84%] Linking CXX executable ../bin/demo_dox_align_global_alignment_banded +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_align_global_alignment_banded.dir/link.txt --verbose=1 +[ 84%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_3_workshop_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102552,6 +102698,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, 6, seqan::BitPacked<> >, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple, 6, seqan::BitPacked<> >]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_3_workshop_solution -lrt -lz -lbz2 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_align_global_alignment_banded.dir/dox/align/global_alignment_banded.cpp.o -o ../bin/demo_dox_align_global_alignment_banded -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_tutorial_iterators_assignment_3_workshop_solution +make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sequences_example_comparisons +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_comparisons.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_dox_align_global_alignment_banded +make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102604,6 +102779,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/pipe.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:42, from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/base.cpp:3: @@ -102656,119 +102833,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/triple_packed.h:82:12: note: because 'seqan::Triple, seqan::Tuple, seqan::Tag >' has user-provided 'seqan::Triple >::Triple(const seqan::Triple >&) [with T1 = long long unsigned int; T2 = seqan::Tuple; T3 = seqan::Tuple]' 82 | inline Triple(Triple const &_p) | ^~~~~~ -[ 83%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorials_custim_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/unassigned_or_unused/tutorials_custim_io/example1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorials_custim_io_example1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Built target demo_unassigned_or_unused_tutorials_custim_io_example1 -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sequence_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution1.cpp -[ 83%] Linking CXX executable ../bin/demo_dox_statistics_build_markov_model -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_statistics_build_markov_model.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o -o ../bin/demo_dox_statistics_build_markov_model -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Built target demo_dox_statistics_build_markov_model -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake --color= -[ 83%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o -o ../bin/demo_tutorial_index_iterators_index_assignment2 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_indices_assignment_2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_index_iterators_index_assignment2 -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_iterators_assignment_3_workshop_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_3_workshop_solution.cpp -[ 84%] Linking CXX executable ../bin/demo_dox_misc_enumerate_strings -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_misc_enumerate_strings.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_misc_enumerate_strings.dir/dox/misc/enumerate_strings.cpp.o -o ../bin/demo_dox_misc_enumerate_strings -lrt -lz -lbz2 -[ 84%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/tutorial/iterators/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_1_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/link.txt --verbose=1 -[ 84%] Built target demo_dox_misc_enumerate_strings -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_1_solution -lrt -lz -lbz2 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_iterators_assignment_1_solution -make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake --color= -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_banded -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend.internal". -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_banded.cpp -Scanning dependencies of target demo_howto_align_gaps_clipping -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Building CXX object demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/howto/align_gaps_clipping.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_genome_annotations_assignment_1_solution -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_iterators_assignment_4_workshop_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Linking CXX executable ../bin/demo_dox_find_finder_index -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_index.dir/link.txt --verbose=1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_4_workshop_solution.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o -o ../bin/demo_dox_find_finder_index -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_dox_find_finder_index -make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend.internal". -Scanning dependencies of target demo_tutorial_iterators_sequence_iterator_demo +Scanning dependencies of target demo_tutorial_journaled_set_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/sequence_iterator_demo.cpp -[ 84%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution5 +[ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/tutorial/journaled_set/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_base.dir/tutorial/journaled_set/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/base.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution1.cpp:1: @@ -102796,8 +102866,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution5 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution1.cpp:1: @@ -102853,6 +102921,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; TSource = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder, seqan::Alloc<> >, seqan::IndexEsa<> > >; typename seqan::Parameter_::Type>::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [6]; seqan::FinderMlr = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [6]]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:12:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:2: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void]' + 429 | Index(Index const &other): + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution1.cpp:1: @@ -102988,134 +103077,78 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_simple_rna_seq_genequant_solution5 -make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend.internal". -[ 84%] Linking CXX executable ../bin/demo_tutorial_indices_find2_index_approx -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/link.txt --verbose=1 -Scanning dependencies of target demo_tutorial_sequences_example_comparisons -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o -o ../bin/demo_tutorial_indices_find2_index_approx -lrt -lz -lbz2 -[ 84%] Building CXX object demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequences/example_comparisons.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; TSource = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; TValue2 = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >; typename seqan::Reference > >::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder, seqan::Alloc<> >, seqan::IndexEsa<> > >; typename seqan::Parameter_::Type>::Type = seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index_esa.h:59:46: required from 'void seqan::_findFirstIndex(seqan::Finder, TSpecFinder>&, const TPattern&, FinderMlr) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [6]; seqan::FinderMlr = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:275:28: required from 'bool seqan::find(seqan::Finder, TSpecFinder>&, const TPattern&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = seqan::IndexEsa<>; TSpecFinder = const seqan::Tag; TPattern = char [6]]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:12:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >& seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >::operator=(const seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:137, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/indices/assignment_2.cpp:2: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_esa_base.h:429:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::IndexEsa<> >' has user-provided 'seqan::Index >::Index(const seqan::Index >&) [with TText = seqan::String, seqan::Alloc<> >; TSpec = void]' - 429 | Index(Index const &other): - | ^~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_indices_find2_index_approx -make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_set_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/tutorial/journaled_set/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_base.dir/tutorial/journaled_set/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/base.cpp +[ 86%] Linking CXX executable ../bin/demo_tutorial_sequences_example_comparisons +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/link.txt --verbose=1 [ 86%] Linking CXX executable ../bin/demo_tutorial_journaled_set_base cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o -o ../bin/demo_tutorial_sequences_example_comparisons -lrt -lz -lbz2 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_base.dir/tutorial/journaled_set/base.cpp.o -o ../bin/demo_tutorial_journaled_set_base -lrt -lz -lbz2 -[ 86%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_3_workshop_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 86%] Linking CXX executable ../bin/demo_tutorial_iterators_sequence_iterator_demo -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/tutorial/iterators/assignment_3_workshop_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_3_workshop_solution -lrt -lz -lbz2 -[ 86%] Built target demo_tutorial_journaled_set_base +[ 86%] Built target demo_tutorial_sequences_example_comparisons make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/depend -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o -o ../bin/demo_tutorial_iterators_sequence_iterator_demo -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/DependInfo.cmake --color= -[ 86%] Linking CXX executable ../bin/demo_tutorial_sequences_example_comparisons Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/depend.internal". -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/tutorial/sequences/example_comparisons.cpp.o -o ../bin/demo_tutorial_sequences_example_comparisons -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_journaled_set_example_join make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/tutorial/journaled_set/example_join.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_example_join.dir/tutorial/journaled_set/example_join.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp -[ 86%] Built target demo_tutorial_iterators_sequence_iterator_demo -[ 86%] Built target demo_tutorial_iterators_assignment_3_workshop_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 86%] Built target demo_tutorial_journaled_set_base make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/depend -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/depend.internal". -[ 86%] Built target demo_tutorial_sequences_example_comparisons -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend.internal". -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend.internal". +[ 86%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_4_workshop_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_4_workshop_solution -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_sequence_io_solution3 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 86%] Built target demo_tutorial_iterators_assignment_4_workshop_solution +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake --color= +[ 86%] Linking CXX executable ../bin/demo_tutorial_iterators_sequence_iterator_demo +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/link.txt --verbose=1 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend.internal". +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/tutorial/iterators/sequence_iterator_demo.cpp.o -o ../bin/demo_tutorial_iterators_sequence_iterator_demo -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_journaled_set_example_journal_string_basic -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp [ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/tutorial/journaled_set/example_journal_string_basic.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/tutorial/journaled_set/example_journal_string_basic.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_journal_string_basic.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 86%] Built target demo_tutorial_iterators_sequence_iterator_demo +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend.internal". Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step6 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 86%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp.o -[ 86%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_4_workshop_solution cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/tutorial/iterators/assignment_4_workshop_solution.cpp.o -o ../bin/demo_tutorial_iterators_assignment_4_workshop_solution -lrt -lz -lbz2 +[ 86%] Linking CXX executable ../bin/demo_tutorial_genome_annotations_assignment_1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/tutorial/genome_annotations/assignment_1_solution.cpp.o -o ../bin/demo_tutorial_genome_annotations_assignment_1_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 86%] Built target demo_tutorial_iterators_assignment_4_workshop_solution +[ 86%] Linking CXX executable ../bin/demo_howto_align_gaps_clipping +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_align_gaps_clipping.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o -o ../bin/demo_howto_align_gaps_clipping -lrt -lz -lbz2 +[ 86%] Built target demo_tutorial_genome_annotations_assignment_1_solution make -f demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build.make demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/DependInfo.cmake --color= @@ -103125,29 +103158,26 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build.make demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 87%] Building CXX object demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/dox/basic/simple_type_construction.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_basic_simple_type_construction.dir/dox/basic/simple_type_construction.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/basic/simple_type_construction.cpp -[ 87%] Linking CXX executable ../bin/demo_tutorial_indices_assignment_2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_assignment_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o -o ../bin/demo_tutorial_indices_assignment_2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_indices_assignment_2 +[ 87%] Built target demo_howto_align_gaps_clipping make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/DependInfo.cmake --color= -[ 87%] Linking CXX executable ../bin/demo_howto_align_gaps_clipping Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/depend.internal". -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_howto_align_gaps_clipping.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_howto_align_gaps_clipping.dir/howto/align_gaps_clipping.cpp.o -o ../bin/demo_howto_align_gaps_clipping -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_journaled_set_example_online_search_assignment1_hint make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp +[ 87%] Linking CXX executable ../bin/demo_tutorial_indices_assignment_2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_assignment_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_assignment_2.dir/tutorial/indices/assignment_2.cpp.o -o ../bin/demo_tutorial_indices_assignment_2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_howto_align_gaps_clipping +[ 87%] Built target demo_tutorial_indices_assignment_2 make -f demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/DependInfo.cmake --color= @@ -103159,6 +103189,22 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 87%] Building CXX object demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/dox/graph_algorithms/topological_sort.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/dox/graph_algorithms/topological_sort.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/graph_algorithms/topological_sort.cpp +[ 87%] Linking CXX executable ../bin/demo_dox_basic_simple_type_construction +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_simple_type_construction.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_simple_type_construction.dir/dox/basic/simple_type_construction.cpp.o -o ../bin/demo_dox_basic_simple_type_construction -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_dox_basic_simple_type_construction +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, @@ -103178,8 +103224,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 87%] Linking CXX executable ../bin/demo_dox_basic_simple_type_construction -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_basic_simple_type_construction.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -103208,7 +103252,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_basic_simple_type_construction.dir/dox/basic/simple_type_construction.cpp.o -o ../bin/demo_dox_basic_simple_type_construction -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -103232,19 +103275,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +[ 87%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_banded +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_banded -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_dox_basic_simple_type_construction -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend +[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_banded +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment3_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment1.cpp +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment3_solution.cpp +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 66 | itGapsPattern = begin(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 67 | itGapsEnd = end(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: @@ -103300,6 +103363,32 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -103355,6 +103444,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::basic_ostream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:38:81: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 125 | data_iterator(other_.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -103379,37 +103487,36 @@ 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:10:48: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -103437,7 +103544,7 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -103462,114 +103569,53 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:66:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 66 | itGapsPattern = begin(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:67:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 67 | itGapsEnd = end(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h: In instantiation of 'seqan::Iter >::Iter(const seqan::Iter >&) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_stream.h:1085:63: required from 'typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type seqan::write(TTarget&, const TContainer&) [with TTarget = seqan::Iter, seqan::StreamIterator > >; TContainer = seqan::Segment >, seqan::InfixSegment>; typename seqan::EnableIf >, seqan::And >, seqan::Not::Type> > > > >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:789:10: required from 'TStream& seqan::operator<<(TStream&, const seqan::Segment&) [with TStream = std::basic_ostream; THost = const seqan::String >; TSpec = seqan::InfixSegment]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence_journaled/sequence_journaled.h:385:20: required from 'TStream& seqan::operator<<(TStream&, const seqan::String >&) [with TStream = std::basic_ostream; TValue = char; THostSpec = seqan::Alloc<>; TJournalSpec = seqan::SortedArray; TBufferSpec = seqan::Alloc<>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:38:81: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:125:49: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 125 | data_iterator(other_.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_set.h:45, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:10:48: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sequence_io/solution3.cpp:1: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:94, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: @@ -103597,6 +103643,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment >, seqan::InfixSegment>; TIterator = const char*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +[ 87%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_journal_string_basic +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/tutorial/journaled_set/example_journal_string_basic.cpp.o -o ../bin/demo_tutorial_journaled_set_example_journal_string_basic -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_tutorial_journaled_set_example_journal_string_basic +make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_join.cpp:3: @@ -103618,6 +103672,30 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const seqan::String >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend.internal". +Scanning dependencies of target demo_dox_seq_io_fai_index_example +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build +[ 87%] Linking CXX executable ../bin/demo_dox_find_finder_index +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_index.dir/link.txt --verbose=1 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Building CXX object demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seq_io/fai_index_example.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_index.dir/dox/find/finder_index.cpp.o -o ../bin/demo_dox_find_finder_index -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_dox_find_finder_index +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend.internal". +Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment4 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp:3: @@ -103728,6 +103806,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 87%] Linking CXX executable ../bin/demo_dox_statistics_build_markov_model +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_statistics_build_markov_model.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -103751,6 +103831,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_statistics_build_markov_model.dir/dox/statistics/build_markov_model.cpp.o -o ../bin/demo_dox_statistics_build_markov_model -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/example_online_search_assignment1_hint.cpp:3: @@ -103835,9 +103916,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 87%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_banded -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/tutorial/pairwise_sequence_alignment/alignment_banded.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_banded -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_dox_statistics_build_markov_model +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend.internal". +[ 87%] Linking CXX executable ../bin/demo_dox_graph_algorithms_topological_sort +Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/link.txt --verbose=1 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/dox/graph_algorithms/topological_sort.cpp.o -o ../bin/demo_dox_graph_algorithms_topological_sort -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_dox_graph_algorithms_topological_sort +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend.internal". +Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_finder +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_finder.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment1.cpp:3: @@ -103892,6 +103999,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 87%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/tutorial/index_iterators/index_assignment1.cpp.o -o ../bin/demo_tutorial_index_iterators_index_assignment1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment1.cpp:3: @@ -104027,6 +104137,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment1.cpp:3: @@ -104055,83 +104166,98 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 87%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_journal_string_basic -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/tutorial/journaled_set/example_journal_string_basic.cpp.o -o ../bin/demo_tutorial_journaled_set_example_journal_string_basic -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_banded -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend +[ 87%] Built target demo_tutorial_index_iterators_index_assignment1 +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend.internal". +[ 87%] Linking CXX executable ../bin/demo_dox_index_mummy +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_index_mummy.dir/link.txt --verbose=1 +[ 87%] Linking CXX executable ../bin/demo_tutorial_indices_find2_index_approx +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_index_mummy.dir/dox/index/mummy.cpp.o -o ../bin/demo_dox_index_mummy -lrt -lz -lbz2 +Scanning dependencies of target demo_tutorial_journaled_string_tree_journaled_string_tree_base make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/tutorial/indices/find2_index_approx.cpp.o -o ../bin/demo_tutorial_indices_find2_index_approx -lrt -lz -lbz2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment3_solution.cpp +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp +[ 87%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o -o ../bin/demo_tutorial_sequence_io_solution1 -lrt -lz -lbz2 +[ 87%] Linking CXX executable ../bin/demo_tutorial_index_iterators_index_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/tutorial/index_iterators/index_assignment2.cpp.o -o ../bin/demo_tutorial_index_iterators_index_assignment2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_journaled_set_example_journal_string_basic -make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend +[ 87%] Built target demo_tutorial_indices_find2_index_approx +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend.internal". -Scanning dependencies of target demo_dox_seq_io_fai_index_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 87%] Built target demo_tutorial_sequence_io_solution1 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/seq_io/fai_index_example.cpp -[ 87%] Linking CXX executable ../bin/demo_dox_graph_algorithms_topological_sort -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/dox/graph_algorithms/topological_sort.cpp.o -o ../bin/demo_dox_graph_algorithms_topological_sort -lrt -lz -lbz2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake --color= +[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_dox_graph_algorithms_topological_sort -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend +Scanning dependencies of target demo_dox_sequence_UNUSED_prefix +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build +[ 87%] Built target demo_tutorial_index_iterators_index_assignment2 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment4 +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake --color= +[ 88%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_prefix.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend.internal". +[ 88%] Built target demo_dox_index_mummy +make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp -[ 87%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution1.dir/tutorial/sequence_io/solution1.cpp.o -o ../bin/demo_tutorial_sequence_io_solution1 -lrt -lz -lbz2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend.internal". +Scanning dependencies of target demo_tutorial_metafunctions_assignment1_solution make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_sequence_io_solution1 -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend +make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution3 +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/metafunctions/assignment1_solution.cpp +Scanning dependencies of target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp -[ 87%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step6 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step6 -lrt -lz -lbz2 +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp +[ 89%] Linking CXX executable ../bin/demo_tutorial_simple_rna_seq_genequant_solution5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/tutorial/simple_rna_seq/genequant_solution5.cpp.o -o ../bin/demo_tutorial_simple_rna_seq_genequant_solution5 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step6 -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend +[ 89%] Built target demo_tutorial_simple_rna_seq_genequant_solution5 +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_struct make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_finder.cpp +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_struct.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/dox/seq_io/fai_index_example.cpp:2: @@ -104283,6 +104409,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 89%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step6 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp:3: @@ -104311,6 +104439,7 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/tutorial/pairwise_sequence_alignment/assignment5_step6.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step6 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp:3: @@ -104368,6 +104497,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>; TIterator = seqan::Iter, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::JournaledStringIterSpec > >; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -104391,6 +104545,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step6 +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp:3: @@ -104419,6 +104580,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_unassigned_or_unused_tutorial_file_io_example1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/example1.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp:3: @@ -104471,6 +104664,27 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment4.cpp:3: @@ -104499,84 +104713,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution3.cpp:1: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 87%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_join -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_join.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_join.dir/tutorial/journaled_set/example_join.cpp.o -o ../bin/demo_tutorial_journaled_set_example_join -lrt -lz -lbz2 -[ 87%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o -o ../bin/demo_tutorial_sequence_io_solution3 -lrt -lz -lbz2 +[ 89%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_prefix +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_prefix -lrt -lz -lbz2 +[ 89%] Linking CXX executable ../bin/demo_tutorial_metafunctions_assignment1_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o -o ../bin/demo_tutorial_metafunctions_assignment1_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_dox_sequence_UNUSED_prefix +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_metafunctions_assignment1_solution +make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend.internal". +Scanning dependencies of target demo_tutorial_metafunctions_base +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/metafunctions/base.cpp +Scanning dependencies of target demo_tutorial_seed_and_extend_solution1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/tutorial/seed_and_extend/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/tutorial/seed_and_extend/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -104643,18 +104811,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_journaled_set_example_join -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_sequence_io_solution3 -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -104680,8 +104836,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -104777,12 +104931,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target demo_tutorial_journaled_string_tree_journaled_string_tree_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -104808,8 +104956,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_finder.cpp:3: @@ -104830,10 +104976,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp -[ 87%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -104859,41 +105001,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 87%] Linking CXX executable ../bin/demo_dox_seq_io_fai_index_example -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seq_io_fai_index_example.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o -o ../bin/demo_dox_seq_io_fai_index_example -lrt -lz -lbz2 -[ 87%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_online_search_assignment1_hint -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.o -o ../bin/demo_tutorial_journaled_set_example_online_search_assignment1_hint -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_dox_seq_io_fai_index_example -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend.internal". -Scanning dependencies of target demo_dox_sequence_UNUSED_prefix -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 88%] Building CXX object demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/sequence/UNUSED_prefix.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 88%] Built target demo_tutorial_journaled_set_example_online_search_assignment1_hint -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 88%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp -[ 88%] Linking CXX executable ../bin/demo_dox_sequence_UNUSED_prefix -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/dox/sequence/UNUSED_prefix.cpp.o -o ../bin/demo_dox_sequence_UNUSED_prefix -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -104935,7 +105042,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -104961,12 +105067,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 88%] Built target demo_dox_sequence_UNUSED_prefix -make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h: In instantiation of 'TSize seqan::impl::expandNode(seqan::TraverserImpl >&, TTraversalNode*, TSize, TObserver&, const TProxySelector&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TTraversalNode = seqan::JstTraversalNode, seqan::Alloc<> > > >; TSize = unsigned int; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>; TProxySelector = seqan::Tag]': @@ -104990,9 +105090,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:830:18: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(const seqan::JstTraversalNode, seqan::Alloc<> > > >&)' first required here 830 | auto child = *parentPtr; | ^~~~~ -Scanning dependencies of target demo_tutorial_metafunctions_assignment1_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -105014,9 +105111,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/metafunctions/assignment1_solution.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': @@ -105101,6 +105195,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::Owner > >]' 105 | Iter(Iter const & other_) : | ^~~~ +[ 89%] Linking CXX executable ../bin/demo_tutorial_metafunctions_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_metafunctions_base.dir/link.txt --verbose=1 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:78, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h: In instantiation of 'decltype (seqan::bitScanForward(node.coverage)) seqan::impl::selectProxy(const TTraverserNode&, const SelectValidProxy&) [with TTraverserNode = seqan::JstTraversalNode, seqan::Alloc<> > > >; decltype (seqan::bitScanForward(node.coverage)) = unsigned int; seqan::SelectValidProxy = seqan::Tag]': @@ -105121,6 +105217,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o -o ../bin/demo_tutorial_metafunctions_base -lrt -lz -lbz2 +[ 89%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_example1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_example1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -105145,6 +105245,15 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_join +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_join.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_join.dir/tutorial/journaled_set/example_join.cpp.o -o ../bin/demo_tutorial_journaled_set_example_join -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_metafunctions_base +make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry::TDeltaPos, seqan::DeltaMapEntry::TDeltaRecord, const TCoverage&, seqan::DeltaEndType) [with TRefPos = unsigned int; TStorePos = unsigned int; seqan::DeltaMapEntry::TDeltaPos = unsigned int; seqan::DeltaMapEntry::TDeltaRecord = seqan::Pair >; seqan::DeltaMapEntry::TCoverage = seqan::String >]': @@ -105162,65 +105271,26 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::JstTraversalNode, seqan::Alloc<> > > >*; TParam = seqan::JstTraversalNode, seqan::Alloc<> > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::JstTraversalNode, seqan::Alloc<> > > >*; TParam = seqan::JstTraversalNode, seqan::Alloc<> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_block.h:402:19: required from 'void seqan::appendValue(seqan::String >&, TValue&&, seqan::Tag) [with TTargetValue = seqan::JstTraversalNode, seqan::Alloc<> > > >; unsigned int SPACE = 4096; TValue = seqan::JstTraversalNode, seqan::Alloc<> > > >; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> > > >, seqan::Block<> >&; TSource = seqan::JstTraversalNode, seqan::Alloc<> > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:175:16: required from 'void seqan::impl::pushNode(seqan::TraverserImpl >&, TTraversalNode&&, TObserver&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TTraversalNode = seqan::JstTraversalNode, seqan::Alloc<> > > >; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:926:19: required from 'void seqan::impl::init(seqan::TraverserImpl >&, TObserver&, const seqan::Tag&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>; TProxySelector = seqan::SelectValidProxy_]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser.h:407:15: required from 'void seqan::init(seqan::TraverserImpl >&, TObserver&, const seqan::Tag&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>; TProxySelector = seqan::SelectValidProxy_]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/jst_extension_base.h:282:9: required from 'void seqan::find(seqan::TraverserImpl >&, TAlgorithm&, TDelegate&&, TObserver&) [with TContainer = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TAlgorithm = seqan::JstExtension, seqan::Alloc<> >, seqan::Tag > >; TDelegate = MatchPrinter, seqan::Alloc<> > >, seqan::JstTraversalSpec > >&; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/jst_extension_base.h:306:13: required from 'void seqan::find(seqan::TraverserImpl >&, TAlgorithm&, TDelegate&&) [with TContainer = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TAlgorithm = seqan::JstExtension, seqan::Alloc<> >, seqan::Tag > >; TDelegate = MatchPrinter, seqan::Alloc<> > >, seqan::JstTraversalSpec > >&]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:60:29: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h:51:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 51 | class JstTraversalNode - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(seqan::JstTraversalNode, seqan::Alloc<> > > >&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::DeltaMapEntry*; TSource1 = seqan::DeltaMapEntry*; TSource2 = seqan::DeltaMapEntry*]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::DeltaMapEntry]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = int; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: required from 'typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1136:19: required from 'typename seqan::Size::Type seqan::reserve(T&&, TSize) [with T = seqan::String, seqan::Alloc<> >&; TSize = int; typename seqan::Size::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:795:16: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = int; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_impl.h:619:11: required from 'typename seqan::EnableIf >, void>::Type seqan::insert(seqan::JournaledStringTree&, TPos, const TValue&, const TIds&, TDeltaType) [with TSequence = seqan::String, seqan::Alloc<> >; TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TPos = int; TValue = int; TIds = std::vector; TDeltaType = seqan::Tag; typename seqan::EnableIf >, void>::Type = void]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:42:75: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] - 86 | class DeltaMapEntry - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' - 163 | String & operator =(String const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry&&)' first required here - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend.internal". +[ 89%] Built target demo_unassigned_or_unused_tutorial_file_io_example1 +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_sequence_length +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +Scanning dependencies of target demo_tutorial_multiple_sequence_alignment_consensus +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build +[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:2: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': @@ -105246,6 +105316,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_journaled_set_example_join +make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h: In instantiation of 'TSize seqan::impl::expandNode(seqan::TraverserImpl >&, TTraversalNode*, TSize, TObserver&, const TProxySelector&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TTraversalNode = seqan::JstTraversalNode, seqan::Alloc<> > > >; TSize = unsigned int; TObserver = std::tuple, seqan::Alloc >, seqan::Myers > > >&>; TProxySelector = seqan::Tag]': @@ -105269,6 +105344,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:830:18: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(const seqan::JstTraversalNode, seqan::Alloc<> > > >&)' first required here 830 | auto child = *parentPtr; | ^~~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -105290,6 +105367,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target demo_tutorial_modifiers_UNUSED_modcomplementdna +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::InsertValueToString_::insertValue_(T&, TPosition, TValue&) [with T = seqan::String, seqan::Alloc<> >; TPosition = int; TValue = const seqan::DeltaMapEntry; TExpand = seqan::Tag]': @@ -105316,6 +105397,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1396:33: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(const seqan::DeltaMapEntry&)' first required here 1396 | typename Value::Type temp_copy = _value; //temp copy because resizeSpace could invalidate _value | ^~~~~~~~~ +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/UNUSED_modcomplementdna.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:78, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h: In instantiation of 'typename seqan::Position > >::Type seqan::impl::positionReference(const seqan::TraverserImpl >&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; typename seqan::Position > >::Type = seqan::String, seqan::Alloc<> >]': @@ -105354,6 +105437,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::JstTraversalNode, seqan::Alloc<> > > >*; TParam = seqan::JstTraversalNode, seqan::Alloc<> > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::JstTraversalNode, seqan::Alloc<> > > >*; TParam = seqan::JstTraversalNode, seqan::Alloc<> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_block.h:402:19: required from 'void seqan::appendValue(seqan::String >&, TValue&&, seqan::Tag) [with TTargetValue = seqan::JstTraversalNode, seqan::Alloc<> > > >; unsigned int SPACE = 4096; TValue = seqan::JstTraversalNode, seqan::Alloc<> > > >; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: required from 'void seqan::appendValue(TContainer&&, TSource&&) [with TContainer = seqan::String, seqan::Alloc<> > > >, seqan::Block<> >&; TSource = seqan::JstTraversalNode, seqan::Alloc<> > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:175:16: required from 'void seqan::impl::pushNode(seqan::TraverserImpl >&, TTraversalNode&&, TObserver&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TTraversalNode = seqan::JstTraversalNode, seqan::Alloc<> > > >; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h:926:19: required from 'void seqan::impl::init(seqan::TraverserImpl >&, TObserver&, const seqan::Tag&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>; TProxySelector = seqan::SelectValidProxy_]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser.h:407:15: required from 'void seqan::init(seqan::TraverserImpl >&, TObserver&, const seqan::Tag&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>; TProxySelector = seqan::SelectValidProxy_]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/jst_extension_base.h:282:9: required from 'void seqan::find(seqan::TraverserImpl >&, TAlgorithm&, TDelegate&&, TObserver&) [with TContainer = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TAlgorithm = seqan::JstExtension, seqan::Alloc<> >, seqan::Tag > >; TDelegate = MatchPrinter, seqan::Alloc<> > >, seqan::JstTraversalSpec > >&; TObserver = std::tuple, seqan::Alloc >, seqan::Tag > > >&>]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/jst_extension_base.h:306:13: required from 'void seqan::find(seqan::TraverserImpl >&, TAlgorithm&, TDelegate&&) [with TContainer = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = void; TAlgorithm = seqan::JstExtension, seqan::Alloc<> >, seqan::Tag > >; TDelegate = MatchPrinter, seqan::Alloc<> > >, seqan::JstTraversalSpec > >&]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:60:29: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h:51:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 51 | class JstTraversalNode + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::JstTraversalNode, seqan::Alloc<> > > >::JstTraversalNode(seqan::JstTraversalNode, seqan::Alloc<> > > >&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:76, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h: In instantiation of 'void seqan::impl::create(seqan::JstBuffer_&) [with TJst = seqan::JournaledStringTree, seqan::Alloc<> > >; TSpec = seqan::Tag]': @@ -105374,6 +105486,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::Owner > >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet, seqan::Journaled, seqan::SortedArray, seqan::Alloc<> > >, seqan::Owner > >]' 105 | Iter(Iter const & other_) : | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:61, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::DeltaMapEntry*; TParam = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:511:23: required from 'void seqan::_arrayConstructMoveDefault(TSource1, TSource2, TTarget) [with TTarget = seqan::DeltaMapEntry*; TSource1 = seqan::DeltaMapEntry*; TSource2 = seqan::DeltaMapEntry*]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1055:31: required from 'void seqan::_arrayConstructMovePointer(TValue*, TValue*, TValue*, seqan::False) [with TValue = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:1064:31: required from 'void seqan::arrayConstructMove(TValue*, TValue*, TValue*) [with TValue = seqan::DeltaMapEntry]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1683:27: required from 'void seqan::_reserveStorage(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = int; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1697:20: required from 'typename seqan::Size >::Type seqan::reserve(seqan::String&, TSize_, seqan::Tag) [with TValue = seqan::DeltaMapEntry; TSpec = seqan::Alloc<>; TSize_ = int; TExpand = seqan::TagGenerous_; typename seqan::Size >::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:1136:19: required from 'typename seqan::Size::Type seqan::reserve(T&&, TSize) [with T = seqan::String, seqan::Alloc<> >&; TSize = int; typename seqan::Size::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map.h:795:16: required from 'void seqan::insert(seqan::DeltaMap&, TDeltaPos, const TDeltaValue&, const TCoverage&, const TDeltaType&) [with TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TDeltaPos = int; TDeltaValue = int; TCoverage = seqan::String >; TDeltaType = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_impl.h:619:11: required from 'typename seqan::EnableIf >, void>::Type seqan::insert(seqan::JournaledStringTree&, TPos, const TValue&, const TIds&, TDeltaType) [with TSequence = seqan::String, seqan::Alloc<> >; TConfig = seqan::DefaultJstConfig, seqan::Alloc<> > >; TSpec = seqan::Tag; TPos = int; TValue = int; TIds = std::vector; TDeltaType = seqan::Tag; typename seqan::EnableIf >, void>::Type = void]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:42:75: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/delta_map_entry.h:86:7: warning: implicitly-declared 'seqan::String >::String(const seqan::String >&)' is deprecated [-Wdeprecated-copy] + 86 | class DeltaMapEntry + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:110, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' + 163 | String & operator =(String const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:61, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: note: synthesized method 'seqan::DeltaMapEntry::DeltaMapEntry(seqan::DeltaMapEntry&&)' first required here + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 89%] Linking CXX executable ../bin/demo_tutorial_sequence_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sequence_io_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sequence_io_solution3.dir/tutorial/sequence_io/solution3.cpp.o -o ../bin/demo_tutorial_sequence_io_solution3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree.h:77, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::JstTraversalNode, seqan::Alloc<> > > >*; TParam = seqan::JstTraversalNode, seqan::Alloc<> > > >]': @@ -105456,86 +105601,19 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_packed.h:163:14: note: because 'seqan::String >' has user-provided 'seqan::String >& seqan::String >::operator=(const seqan::String >&) [with TValue = bool; THostspec = seqan::Alloc<>]' 163 | String & operator =(String const & source) | ^~~~~~~~ -[ 89%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution3 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_sam_and_bam_io_solution3 -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_struct -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/link.txt --verbose=1 -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_struct.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment1 -lrt -lz -lbz2 -[ 89%] Linking CXX executable ../bin/demo_tutorial_metafunctions_assignment1_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/tutorial/metafunctions/assignment1_solution.cpp.o -o ../bin/demo_tutorial_metafunctions_assignment1_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_metafunctions_assignment1_solution -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_tutorial_file_io_example1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/tutorial_file_io/example1.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_journaled_set_solution_online_search_assignment1 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_seed_and_extend_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/tutorial/seed_and_extend/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/tutorial/seed_and_extend/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution1.cpp -[ 89%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step3 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 -make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend.internal". -Scanning dependencies of target demo_tutorial_metafunctions_base -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/metafunctions/base.cpp -[ 89%] Linking CXX executable ../bin/demo_unassigned_or_unused_tutorial_file_io_example1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/unassigned_or_unused/tutorial_file_io/example1.cpp.o -o ../bin/demo_unassigned_or_unused_tutorial_file_io_example1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_unassigned_or_unused_tutorial_file_io_example1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend +[ 89%] Built target demo_tutorial_sequence_io_solution3 +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend.internal". -Scanning dependencies of target demo_unassigned_or_unused_sequence_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution1.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:50, from /build/seqan2-2.4.0+dfsg/demos/tutorial/seed_and_extend/solution1.cpp:3: @@ -105546,41 +105624,87 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ -[ 89%] Linking CXX executable ../bin/demo_tutorial_metafunctions_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_metafunctions_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_metafunctions_base.dir/tutorial/metafunctions/base.cpp.o -o ../bin/demo_tutorial_metafunctions_base -lrt -lz -lbz2 +[ 89%] Linking CXX executable ../bin/demo_dox_seq_io_fai_index_example +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_seq_io_fai_index_example.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_seq_io_fai_index_example.dir/dox/seq_io/fai_index_example.cpp.o -o ../bin/demo_dox_seq_io_fai_index_example -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_metafunctions_base -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend +[ 89%] Built target demo_dox_seq_io_fai_index_example +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend.internal". -Scanning dependencies of target demo_tutorial_multiple_sequence_alignment_consensus +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_modifiers_assignment1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/assignment1.cpp +[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_set_example_online_search_assignment1_hint +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/tutorial/journaled_set/example_online_search_assignment1_hint.cpp.o -o ../bin/demo_tutorial_journaled_set_example_online_search_assignment1_hint -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_journaled_set_example_online_search_assignment1_hint +make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend.internal". +Scanning dependencies of target demo_dox_find_finder_aho_corasick +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_aho_corasick.cpp [ 89%] Linking CXX executable ../bin/demo_tutorial_seed_and_extend_solution1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/tutorial/seed_and_extend/solution1.cpp.o -o ../bin/demo_tutorial_seed_and_extend_solution1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 89%] Built target demo_tutorial_seed_and_extend_solution1 -make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend +make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend.internal". -Scanning dependencies of target demo_tutorial_modifiers_UNUSED_modcomplementdna +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend.internal". +Scanning dependencies of target demo_tutorial_modifiers_modreverse make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build +make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/UNUSED_modcomplementdna.cpp -[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o -o ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base -lrt -lz -lbz2 +[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/tutorial/modifiers/modreverse.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_modreverse.dir/tutorial/modifiers/modreverse.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/modreverse.cpp +[ 89%] Linking CXX executable ../bin/demo_tutorial_modifiers_UNUSED_modcomplementdna +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o -o ../bin/demo_tutorial_modifiers_UNUSED_modcomplementdna -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_tutorial_modifiers_UNUSED_modcomplementdna +make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend.internal". +Scanning dependencies of target demo_unassigned_or_unused_sample_seqs +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:44, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:4: +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h: In instantiation of 'bool seqan::convertAlignment(const seqan::Graph >&, seqan::Align&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TSource = seqan::String, seqan::Alloc<> >; TSpec2 = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:579:21: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:40:57: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:994:57: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 994 | for(TSize i = 0; i, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +[ 89%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/tutorial/pairwise_sequence_alignment/assignment5_step3.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5_step3 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp:5: @@ -105605,6 +105729,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 89%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 +make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp:5: @@ -105629,19 +105759,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:44, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:4: -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h: In instantiation of 'bool seqan::convertAlignment(const seqan::Graph >&, seqan::Align&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TSource = seqan::String, seqan::Alloc<> >; TSpec2 = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:579:21: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:40:57: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:994:57: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 994 | for(TSize i = 0; i, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ +Scanning dependencies of target demo_tutorial_modifiers_modview +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 90%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/modview.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp:5: @@ -105709,6 +105832,50 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, FractionalScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FractionalScore = const seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:482:28: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, TStringSet1&, TNames&, const seqan::MsaOptions&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TStringSet1 = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TNames = seqan::String > >; TAlphabet = seqan::SimpleType; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:568:23: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, const TScore&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:578:23: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score >]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:40:57: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1667 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1679 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] + 1701 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp:5: @@ -105759,7 +105926,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sequence_length.cpp:5: @@ -105785,97 +105951,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 89%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/DependInfo.cmake --color= -[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/link.txt --verbose=1 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend.internal". -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o -o ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -lrt -lz -lbz2 -Scanning dependencies of target demo_tutorial_sam_and_bam_io_solution1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution1.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervalsExcludeTouching(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String > > > >; TValue = unsigned int; TCargo = seqan::Pair >]': -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:571:49: required from 'void seqan::matchRefinement(TAlignmentString&, seqan::StringSet&, TScore&, TOutGraph&, typename seqan::Size::Type>::Type, TAnnotation&, seqan::Tag) [with TAlignmentString = seqan::String >; TAnnotation = bool; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >; TScore = unsigned int; TTagSpec = seqan::TagExactRefinement_; typename seqan::Size::Type>::Type = unsigned int]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h:678:20: required from 'void seqan::matchRefinement(TFragmentString&, seqan::StringSet&, TOutGraph&) [with TFragmentString = seqan::String >; TOutGraph = seqan::Graph, seqan::Alloc<> >, seqan::Dependent > >, unsigned int, seqan::Tag > >; TSequence = seqan::String, seqan::Alloc<> >; TSetSpec = seqan::Dependent >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h:136:20: required from 'void seqan::buildAlignmentGraph(seqan::String&, seqan::String&, seqan::Graph >&, FractionalScore) [with TFragment = seqan::Fragment<>; TSpec1 = seqan::Alloc<>; TScoreValue = int; TSpec2 = seqan::Alloc<>; TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = unsigned int; TSpec = seqan::Tag; seqan::FractionalScore = const seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:482:28: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, TStringSet1&, TNames&, const seqan::MsaOptions&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TStringSet1 = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TNames = seqan::String > >; TAlphabet = seqan::SimpleType; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:568:23: required from 'void seqan::globalMsaAlignment(seqan::Graph >&, const TScore&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_msa.h:578:23: required from 'void seqan::globalMsaAlignment(seqan::Align&, const TScore&) [with TSource = seqan::String, seqan::Alloc<> >; TSpec = seqan::Tag; TScore = seqan::Score >]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:40:57: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1667:18: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1667 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1679:23: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1679 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1701:27: warning: implicitly-declared 'seqan::IntervalTreeNode > > >& seqan::IntervalTreeNode > > >::operator=(const seqan::IntervalTreeNode > > >&)' is deprecated [-Wdeprecated-copy] - 1701 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/consensus.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_modifiers_assignment1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Linking CXX executable ../bin/demo_tutorial_modifiers_UNUSED_modcomplementdna -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/link.txt --verbose=1 -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/assignment1.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/tutorial/modifiers/UNUSED_modcomplementdna.cpp.o -o ../bin/demo_tutorial_modifiers_UNUSED_modcomplementdna -lrt -lz -lbz2 +[ 90%] Linking CXX executable ../bin/demo_tutorial_modifiers_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o -o ../bin/demo_tutorial_modifiers_assignment1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_modifiers_UNUSED_modcomplementdna -make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend +[ 90%] Built target demo_tutorial_modifiers_assignment1 +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend.internal". -Scanning dependencies of target demo_dox_find_finder_aho_corasick +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_modifyString make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/find/finder_aho_corasick.cpp -[ 89%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment4 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment4 -lrt -lz -lbz2 +[ 90%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, from /build/seqan2-2.4.0+dfsg/demos/tutorial/sam_and_bam_io/solution1.cpp:1: @@ -105948,72 +106039,14 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 89%] Linking CXX executable ../bin/demo_tutorial_modifiers_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_assignment1.dir/tutorial/modifiers/assignment1.cpp.o -o ../bin/demo_tutorial_modifiers_assignment1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_journaled_set_solution_online_search_assignment4 -make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend.internal". -Scanning dependencies of target demo_tutorial_modifiers_modreverse -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/tutorial/modifiers/modreverse.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_modreverse.dir/tutorial/modifiers/modreverse.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/modreverse.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_modifiers_assignment1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend.internal". -[ 89%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment3_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment3_solution -lrt -lz -lbz2 -Scanning dependencies of target demo_unassigned_or_unused_sample_seqs -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 89%] Built target demo_tutorial_parsing_command_line_arguments_assignment3_solution -make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend.internal". -Scanning dependencies of target demo_tutorial_modifiers_modview -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Building CXX object demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/modifiers/modview.cpp -[ 90%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_finder -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_finder -lrt -lz -lbz2 +[ 90%] Linking CXX executable ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/tutorial/journaled_string_tree/journaled_string_tree_base.cpp.o -o ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base -lrt -lz -lbz2 [ 90%] Linking CXX executable ../bin/demo_tutorial_modifiers_modreverse cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_modreverse.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_modreverse.dir/tutorial/modifiers/modreverse.cpp.o -o ../bin/demo_tutorial_modifiers_modreverse -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 90%] Built target demo_tutorial_modifiers_modreverse -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example_with_modifyString -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Built target demo_tutorial_journaled_set_solution_online_search_finder make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/DependInfo.cmake --color= @@ -106023,24 +106056,69 @@ make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Linking CXX executable ../bin/demo_tutorial_modifiers_modview +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 90%] Building CXX object demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/tutorial/multiple_sequence_alignment/assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_modview.dir/link.txt --verbose=1 cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/tutorial/multiple_sequence_alignment/assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/assignment1.cpp -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o -o ../bin/demo_tutorial_modifiers_modview -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Built target demo_tutorial_modifiers_modview +[ 90%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/depend.internal". +[ 90%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/tutorial/sam_and_bam_io/solution3.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution3 -lrt -lz -lbz2 Scanning dependencies of target demo_tutorial_journaled_set_solution_online_search_assignment2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 91%] Building CXX object demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/tutorial/journaled_set/solution_online_search_assignment2.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/tutorial/journaled_set/solution_online_search_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment2.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 91%] Built target demo_tutorial_sam_and_bam_io_solution3 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp +[ 92%] Linking CXX executable ../bin/demo_tutorial_modifiers_modview +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_modifiers_modview.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_modifiers_modview.dir/tutorial/modifiers/modview.cpp.o -o ../bin/demo_tutorial_modifiers_modview -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Built target demo_tutorial_modifiers_modview +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp +[ 92%] Linking CXX executable ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/tutorial/journaled_string_tree/journaled_string_tree_base_assignment1.cpp.o -o ../bin/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 +make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend.internal". +Scanning dependencies of target demo_tutorial_basics_strings +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/strings.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': @@ -106063,6 +106141,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 92%] Linking CXX executable ../../bin/test_seeds_banded_chain_alignment_interface +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/test_banded_chain_alignment_interface.cpp.o -o ../../bin/test_seeds_banded_chain_alignment_interface -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': @@ -106171,9 +106252,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 91%] Linking CXX executable ../bin/demo_dox_find_finder_aho_corasick -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_aho_corasick.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o -o ../bin/demo_dox_find_finder_aho_corasick -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/sample_seqs.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': @@ -106220,38 +106298,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 92%] Linking CXX executable ../bin/demo_dox_find_finder_aho_corasick +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_find_finder_aho_corasick.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_find_finder_aho_corasick.dir/dox/find/finder_aho_corasick.cpp.o -o ../bin/demo_dox_find_finder_aho_corasick -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 91%] Built target demo_dox_find_finder_aho_corasick -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend +[ 92%] Built target test_seeds_banded_chain_alignment_interface +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp -[ 93%] Linking CXX executable ../bin/demo_unassigned_or_unused_sequence_length -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o -o ../bin/demo_unassigned_or_unused_sequence_length -lrt -lz -lbz2 +[ 92%] Built target demo_dox_find_finder_aho_corasick +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_unassigned_or_unused_sequence_length -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend.internal". +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp +Scanning dependencies of target demo_tutorial_string_sets_example_functionality make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp -[ 93%] Linking CXX executable ../bin/demo_tutorial_indices_base -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_base.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o -o ../bin/demo_tutorial_indices_base -lrt -lz -lbz2 +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/tutorial/string_sets/example_functionality.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/tutorial/string_sets/example_functionality.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/example_functionality.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa.h:44, from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/assignment1.cpp:4: /build/seqan2-2.4.0+dfsg/include/seqan/graph_msa/graph_align_tcoffee_base.h: In instantiation of 'bool seqan::convertAlignment(const seqan::Graph >&, seqan::Align&) [with TStringSet = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TCargo = void; TSpec = const seqan::Tag; TSource = seqan::String, seqan::Alloc<> >; TSpec2 = seqan::Tag]': @@ -106265,6 +106340,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::Tag >]' 91 | Iter(Iter const & other) : | ^~~~ +[ 92%] Linking CXX executable ../bin/demo_tutorial_basics_strings +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_strings.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o -o ../bin/demo_tutorial_basics_strings -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/demos/tutorial/multiple_sequence_alignment/assignment1.cpp:3: @@ -106309,6 +106387,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode > > >' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo > >]' 288 | IntervalTreeNode(IntervalTreeNode const & other) : | ^~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Built target demo_tutorial_basics_strings +make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend.internal". +Scanning dependencies of target demo_dox_pipe_pool_sorter +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/pipe/pool_sorter.cpp +[ 92%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/tutorial/journaled_set/solution_online_search_assignment1.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment1 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment2.cpp:3: @@ -106391,6 +106485,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Built target demo_tutorial_journaled_set_solution_online_search_assignment1 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment2.cpp:3: @@ -106419,6 +106518,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -106470,6 +106571,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/demos/tutorial/journaled_set/solution_online_search_assignment2.cpp:3: @@ -106526,83 +106633,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 92%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment3_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/tutorial/parsing_command_line_arguments/assignment3_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment3_solution -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_tutorial_indices_base -make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend.internal". -Scanning dependencies of target demo_tutorial_basics_strings -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/basics/strings.cpp -[ 93%] Linking CXX executable ../bin/demo_tutorial_basics_strings -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_basics_strings.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_basics_strings.dir/tutorial/basics/strings.cpp.o -o ../bin/demo_tutorial_basics_strings -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_tutorial_basics_strings -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp -[ 93%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/DependInfo.cmake --color= -[ 93%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution1 -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend.internal". -Scanning dependencies of target demo_tutorial_string_sets_example_functionality -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/tutorial/string_sets/example_functionality.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/tutorial/string_sets/example_functionality.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/example_functionality.cpp -[ 93%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_struct -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_struct -lrt -lz -lbz2 -[ 93%] Built target demo_tutorial_sam_and_bam_io_solution1 -make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend.internal". -Scanning dependencies of target demo_dox_pipe_pool_sorter -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/dox/pipe/pool_sorter.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_tutorial_parsing_command_line_arguments_example_with_struct -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend +[ 92%] Built target demo_tutorial_parsing_command_line_arguments_assignment3_solution +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend.internal". +Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp +[ 92%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp +[ 93%] Linking CXX executable ../bin/demo_unassigned_or_unused_sequence_length +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/unassigned_or_unused/sequence_length.cpp.o -o ../bin/demo_unassigned_or_unused_sequence_length -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:183, from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp:3: /build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_myers_hirschberg_impl.h: In instantiation of 'int seqan::_globalAlignment(seqan::Gaps&, seqan::Gaps&, const MyersHirschberg&) [with TSequenceH = seqan::String, seqan::Alloc<> >; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; seqan::MyersHirschberg = seqan::Tag]': @@ -106670,75 +106719,39 @@ cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/tutorial/string_sets/example_functionality.cpp.o -o ../bin/demo_tutorial_string_sets_example_functionality -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Linking CXX executable ../bin/demo_dox_pipe_pool_sorter -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_pipe_pool_sorter.dir/link.txt --verbose=1 [ 93%] Built target demo_tutorial_string_sets_example_functionality -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake --color= -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o -o ../bin/demo_dox_pipe_pool_sorter -lrt -lz -lbz2 -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend.internal". -Scanning dependencies of target demo_tutorial_pairwise_sequence_alignment_assignment5 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Building CXX object demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_dox_pipe_pool_sorter make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/depend +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/DependInfo.cmake --color= +[ 93%] Built target demo_unassigned_or_unused_sequence_length +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/depend.internal". -Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment5_solution -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment5_solution.cpp -[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend.internal". +Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_assignment5_solution +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_tutorial_iterators_assignment_1 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/assignment5_solution.cpp [ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/tutorial/iterators/assignment_1.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_iterators_assignment_1.dir/tutorial/iterators/assignment_1.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/iterators/assignment_1.cpp -[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment1.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 +[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/DependInfo.cmake --color= -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp: In function 'int main()': -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:71:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 71 | itGapsPattern = begin(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ -/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:72:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] - 72 | itGapsEnd = end(gapsPattern); - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' - 91 | Iter(Iter const & other) : - | ^~~~ Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/depend.internal". Scanning dependencies of target demo_tutorial_parsing_command_line_arguments_example1_detailed @@ -106747,11 +106760,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/tutorial/parsing_command_line_arguments/example1_detailed.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/tutorial/parsing_command_line_arguments/example1_detailed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/parsing_command_line_arguments/example1_detailed.cpp -[ 94%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_1.dir/tutorial/iterators/assignment_1.cpp.o -o ../bin/demo_tutorial_iterators_assignment_1 -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/tutorial/journaled_set/solution_online_search_assignment4.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment4 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Built target demo_tutorial_iterators_assignment_1 +[ 94%] Built target demo_tutorial_journaled_set_solution_online_search_assignment4 make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/DependInfo.cmake --color= @@ -106763,11 +106776,11 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/tutorial/string_sets/example_functionality_2.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/tutorial/string_sets/example_functionality_2.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/string_sets/example_functionality_2.cpp -[ 94%] Linking CXX executable ../bin/demo_unassigned_or_unused_sample_seqs -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o -o ../bin/demo_unassigned_or_unused_sample_seqs -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_dox_pipe_pool_sorter +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_dox_pipe_pool_sorter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_dox_pipe_pool_sorter.dir/dox/pipe/pool_sorter.cpp.o -o ../bin/demo_dox_pipe_pool_sorter -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Built target demo_unassigned_or_unused_sample_seqs +[ 94%] Built target demo_dox_pipe_pool_sorter make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/DependInfo.cmake --color= @@ -106779,162 +106792,179 @@ make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/tutorial/pattern_matching/assignment3.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/tutorial/pattern_matching/assignment3.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp -[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap -lrt -lz -lbz2 -[ 95%] Linking CXX executable ../bin/demo_tutorial_string_sets_example_functionality_2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/tutorial/string_sets/example_functionality_2.cpp.o -o ../bin/demo_tutorial_string_sets_example_functionality_2 -lrt -lz -lbz2 +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp: In function 'int main()': +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:71:42: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 71 | itGapsPattern = begin(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +/build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:72:36: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >& seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >::operator=(const seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >&)' is deprecated [-Wdeprecated-copy] + 72 | itGapsEnd = end(gapsPattern); + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:86, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pairwise_sequence_alignment/assignment5.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_array.h:91:5: note: because 'seqan::Iter >, seqan::Tag >, seqan::GapsIterator > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::Tag >]' + 91 | Iter(Iter const & other) : + | ^~~~ +[ 94%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/tutorial/journaled_set/solution_online_search_finder.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_finder -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_tutorial_iterators_assignment_1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_iterators_assignment_1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_iterators_assignment_1.dir/tutorial/iterators/assignment_1.cpp.o -o ../bin/demo_tutorial_iterators_assignment_1 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_string_sets_example_functionality_2 +[ 94%] Built target demo_tutorial_iterators_assignment_1 make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/depend.internal". -[ 95%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 94%] Built target demo_tutorial_journaled_set_solution_online_search_finder make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/depend.internal". -Scanning dependencies of target demo_tutorial_a_first_example_basic_code_detailed -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_unassigned_or_unused_bam_print_alignments make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/tutorial/a_first_example/basic_code_detailed.cpp.o -[ 95%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/unassigned_or_unused/bam_print_alignments.cpp.o +Scanning dependencies of target demo_tutorial_a_first_example_basic_code_detailed +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build +[ 94%] Building CXX object demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/unassigned_or_unused/bam_print_alignments.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/unassigned_or_unused/bam_print_alignments.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_print_alignments.cpp +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/tutorial/a_first_example/basic_code_detailed.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/tutorial/a_first_example/basic_code_detailed.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/a_first_example/basic_code_detailed.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index >, seqan::IndexQGram, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram, seqan::Tag >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram, seqan::Tag > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' -/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:569:26: required from 'typename seqan::InfixOnValue::Type seqan::infix(seqan::Finder&) [with THaystack = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TSpec = const seqan::Tag; typename seqan::InfixOnValue::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:18:105: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::IndexQGram, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] - 110 | target = source; - | ~~~~~~~^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, - from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::String >; TShapeSpec = seqan::UngappedShape<4>]' - 143 | Index(Index const &other): - | ^~~~~ -[ 95%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5 -lrt -lz -lbz2 -[ 95%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_consensus -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_consensus -lrt -lz -lbz2 -[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_modifyString -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_modifyString -lrt -lz -lbz2 -[ 95%] Linking CXX executable ../bin/demo_tutorial_a_first_example_basic_code_detailed -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/tutorial/a_first_example/basic_code_detailed.cpp.o -o ../bin/demo_tutorial_a_first_example_basic_code_detailed -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment3.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_a_first_example_basic_code_detailed +[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/DependInfo.cmake --color= -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/depend.internal". -[ 95%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5 +Scanning dependencies of target demo_tutorial_graph_graph_algo_scc +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_algo_scc.cpp +[ 94%] Linking CXX executable ../bin/demo_tutorial_sam_and_bam_io_solution1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/tutorial/sam_and_bam_io/solution1.cpp.o -o ../bin/demo_tutorial_sam_and_bam_io_solution1 -lrt -lz -lbz2 +[ 94%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_struct +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/tutorial/parsing_command_line_arguments/example_with_struct.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_struct -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 94%] Built target demo_tutorial_sam_and_bam_io_solution1 make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/depend.internal". -Scanning dependencies of target demo_tutorial_graph_graph_algo_scc -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target demo_tutorial_pattern_matching_find_approx -[ 95%] Building CXX object demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/graph/graph_algo_scc.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/tutorial/pattern_matching/find_approx.cpp.o +[ 94%] Building CXX object demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/tutorial/pattern_matching/find_approx.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/c++ -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/tutorial/pattern_matching/find_approx.cpp.o -c /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/find_approx.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example_with_modifyString +[ 94%] Built target demo_tutorial_parsing_command_line_arguments_example_with_struct make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend +[ 94%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/link.txt --verbose=1 make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/alf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake --color= +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/tutorial/pairwise_sequence_alignment/alignment_global_assignment2.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 -lrt -lz -lbz2 Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/alf.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/alf.dir/depend.internal". -[ 95%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment2 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/tutorial/journaled_set/solution_online_search_assignment2.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment2 -lrt -lz -lbz2 Scanning dependencies of target alf make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/alf/CMakeFiles/alf.dir/alf.cpp.o +[ 94%] Building CXX object apps/alf/CMakeFiles/alf.dir/alf.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/alf.dir/alf.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_multiple_sequence_alignment_consensus +[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/depend.internal". -[ 95%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment3 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/link.txt --verbose=1 Scanning dependencies of target four2three -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/tutorial/pattern_matching/assignment3.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment3 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o +[ 94%] Building CXX object apps/bs_tools/CMakeFiles/four2three.dir/four2three.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/four2three.dir/four2three.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp +[ 95%] Linking CXX executable ../bin/demo_tutorial_string_sets_example_functionality_2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/tutorial/string_sets/example_functionality_2.cpp.o -o ../bin/demo_tutorial_string_sets_example_functionality_2 -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_journaled_set_solution_online_search_assignment2 +[ 95%] Built target demo_tutorial_string_sets_example_functionality_2 make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/casbar.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/casbar.dir/depend.internal". +Scanning dependencies of target casbar make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_pattern_matching_assignment3 +make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/casbar.dir/casbar.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:41, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h: In instantiation of 'typename seqan::DisableIf > >::Type seqan::assign(TTarget&, TSource&) [with TTarget = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TSource = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; typename seqan::DisableIf > >::Type = void]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:645:15: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TValue2 = seqan::Index >, seqan::IndexQGram, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:594:19: required from 'void seqan::create(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:863:15: required from 'typename seqan::Reference > >::Type seqan::value(seqan::Holder >&) [with TValue = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; typename seqan::Reference > >::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/index/find_index.h:115:21: required from 'typename seqan::Parameter_ >::Type seqan::container(seqan::Finder, TSpecFinder>&) [with TText = seqan::String >; TSpec = seqan::IndexQGram, seqan::Tag >; TSpecFinder = const seqan::Tag; typename seqan::Parameter_ >::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:904:21: required from 'typename seqan::Parameter_::Type>::Type seqan::haystack(TObject&) [with TObject = seqan::Finder >, seqan::IndexQGram, seqan::Tag > > >; typename seqan::Parameter_::Type>::Type = seqan::Index >, seqan::IndexQGram, seqan::Tag > >&]' +/build/seqan2-2.4.0+dfsg/include/seqan/find/find_base.h:569:26: required from 'typename seqan::InfixOnValue::Type seqan::infix(seqan::Finder&) [with THaystack = seqan::Index >, seqan::IndexQGram, seqan::Tag > >; TSpec = const seqan::Tag; typename seqan::InfixOnValue::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:18:105: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/fundamental_transport.h:110:12: warning: implicitly-declared 'seqan::Index >, seqan::IndexQGram, seqan::Tag > >& seqan::Index >, seqan::IndexQGram, seqan::Tag > >::operator=(const seqan::Index >, seqan::IndexQGram, seqan::Tag > >&)' is deprecated [-Wdeprecated-copy] + 110 | target = source; + | ~~~~~~~^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:92, + from /build/seqan2-2.4.0+dfsg/demos/tutorial/pattern_matching/assignment3.cpp:3: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::String >; TShapeSpec = seqan::UngappedShape<4>]' + 143 | Index(Index const &other): + | ^~~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_a_first_example_basic_code_detailed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/tutorial/a_first_example/basic_code_detailed.cpp.o -o ../bin/demo_tutorial_a_first_example_basic_code_detailed -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_a_first_example_basic_code_detailed make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake --color= Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/depend.internal". Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/depend.internal". -Scanning dependencies of target casbar -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Scanning dependencies of target bisar make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/bs_tools/CMakeFiles/casbar.dir/casbar.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/casbar.dir/casbar.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp [ 95%] Building CXX object apps/bs_tools/CMakeFiles/bisar.dir/bisar.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/bisar.dir/bisar.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, @@ -107035,6 +107065,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_assignment3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/tutorial/pattern_matching/assignment3.cpp.o -o ../bin/demo_tutorial_pattern_matching_assignment3 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/demos/unassigned_or_unused/bam_print_alignments.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -107077,6 +107110,11 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_pattern_matching_assignment3 +make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -107102,6 +107140,8 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, @@ -107127,33 +107167,92 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target dfi +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/dfi.dir/dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp +[ 95%] Linking CXX executable ../bin/demo_unassigned_or_unused_sample_seqs +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/unassigned_or_unused/sample_seqs.cpp.o -o ../bin/demo_unassigned_or_unused_sample_seqs -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_unassigned_or_unused_sample_seqs +make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend.internal". +Scanning dependencies of target fx_fastq_stats +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/link.txt --verbose=1 +[ 95%] Building CXX object apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/tutorial/pairwise_sequence_alignment/alignment_global_overlap.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend.internal". +Scanning dependencies of target fx_bam_coverage +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp [ 95%] Linking CXX executable ../bin/demo_tutorial_pattern_matching_find_approx cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/tutorial/pattern_matching/find_approx.cpp.o -o ../bin/demo_tutorial_pattern_matching_find_approx -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 95%] Built target demo_tutorial_pattern_matching_find_approx -make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend +make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/depend.internal". -Scanning dependencies of target dfi +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake --color= +[ 95%] Linking CXX executable ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/tutorial/pairwise_sequence_alignment/assignment5.cpp.o -o ../bin/demo_tutorial_pairwise_sequence_alignment_assignment5 -lrt -lz -lbz2 +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend.internal". +Scanning dependencies of target gustaf_mate_joining make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build +make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/dfi/CMakeFiles/dfi.dir/dfi.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/dfi.dir/dfi.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +[ 95%] Building CXX object apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp +[ 95%] Linking CXX executable ../bin/demo_tutorial_graph_graph_algo_scc +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o -o ../bin/demo_tutorial_graph_graph_algo_scc -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5 +make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_graph_graph_algo_scc +make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/depend.internal". +Scanning dependencies of target gustaf +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/gustaf.dir/gustaf.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp +Scanning dependencies of target insegt +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/insegt.dir/insegt.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: @@ -107178,9 +107277,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 95%] Linking CXX executable ../bin/demo_tutorial_graph_graph_algo_scc -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/tutorial/graph/graph_algo_scc.cpp.o -o ../bin/demo_tutorial_graph_graph_algo_scc -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: @@ -107207,33 +107303,140 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/statistics.h:41, + from /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free.h:47, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:49: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:42:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/statistics.h:41, - from /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free.h:47, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:49: + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) @@ -107244,8 +107447,9 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' @@ -107266,6 +107470,104 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free.h:59, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:49: +/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h: In instantiation of 'void seqan::_alignmentFreeComparison(seqan::Matrix&, const TStringSet&, const seqan::AFScore >&) [with TValue = double; TStringSet = seqan::StringSet, seqan::Alloc<> > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/alignment_free_comparison.h:101:29: required from 'void seqan::alignmentFreeComparison(seqan::Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = seqan::StringSet, seqan::Alloc<> > >; TValue = double; TComparisonMethod = seqan::AFScore >]' +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:188:67: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h:189:34: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); + | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_indices_base +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_indices_base.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_indices_base.dir/tutorial/indices/base.cpp.o -o ../bin/demo_tutorial_indices_base -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:41: @@ -107300,28 +107602,31 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_graph_graph_algo_scc -make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake --color= +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: @@ -107347,21 +107652,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_indices_base +make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake --color= In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -107369,12 +107678,43 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/depend.internal". +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:28, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +Scanning dependencies of target mason_variator +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:37: @@ -107393,38 +107733,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' 112 | Iter const & operator = (Iter const & other_) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -107432,36 +107756,27 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:42:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: @@ -107488,27 +107803,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target fx_fastq_stats -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.h:41:23: required from 'bool preProcess(TOptions&) [with TOptions = AppOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:146:23: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -107516,7 +107824,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/four2three.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -107548,36 +107856,34 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h:21:14: required from 'bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.h:996:27: required from 'bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:294:47: required from here +/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -107601,24 +107907,40 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/alignment_free.h:59, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:49: -/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h: In instantiation of 'void seqan::_alignmentFreeComparison(seqan::Matrix&, const TStringSet&, const seqan::AFScore >&) [with TValue = double; TStringSet = seqan::StringSet, seqan::Alloc<> > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/alignment_free_comparison.h:101:29: required from 'void seqan::alignmentFreeComparison(seqan::Matrix&, const TStringSet&, const TComparisonMethod&) [with TStringSet = seqan::StringSet, seqan::Alloc<> > >; TValue = double; TComparisonMethod = seqan::AFScore >]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:188:67: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/alignment_free/af_n2.h:189:34: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 189 | itStandardisedKmerCounts = begin(standardisedKmerCounts); - | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >]' - 105 | Iter(Iter const & other_) : - | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example_with_modifyString +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/tutorial/parsing_command_line_arguments/example_with_modifyString.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example_with_modifyString -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -107642,9 +107964,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example_with_modifyString +make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/depend.internal". +Scanning dependencies of target mason_genome +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -107654,45 +107989,24 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -107703,45 +108017,53 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here +/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -107753,17 +108075,19 @@ 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -107771,147 +108095,243 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here +/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar_base.h:21:14: required from 'bool loadReadsCroppedId(seqan::FragmentStore&, TFileName&) [with TFSSpec = seqan::MyFragmentStoreConfig; TFSConfig = seqan::FragmentStoreConfig; TFileName = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.h:996:27: required from 'bool postProcessMain(TOptions&, const TModel&) [with TOptions = AppOptions; TModel = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:294:47: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/bisar.cpp:39: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here +/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:873:31: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h: In instantiation of 'void seqan::createReadCountGFF(TFile&, TReadAnnoStore&, seqan::FragmentStore&) [with TFile = std::basic_fstream; TReadAnnoStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]': +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:889:23: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:75:14: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 75 | itAnnoIds = begin(getValue(itCountStore).annoIds); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:76:17: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 76 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:100:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 100 | itAnnoIds = begin(getValue(itCountStore).annoIds); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:101:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 101 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:134:16: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 134 | itAnnoIds = begin(getValue(itCountStore).annoIds); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:135:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 135 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:169:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 169 | itAnnoIds = begin(getValue(itCountStore).annoIds); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: +/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:170:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 170 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:899:31: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:164:40: required from here +/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:45: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/alf/alf.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -107919,199 +108339,263 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:17: +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeDown(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:48:64: required from 'void seqan::adjustParentEntries(seqan::FragmentStore&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:851:21: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 853 | Iter > tmp(it); + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1355:36: required from 'void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:755:36: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] + 855 | return tmp; + | ^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' + 272 | operator = (Iter const &_origin) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::getIdsForRead(TAnnoIds&, seqan::FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TIntervalTree = seqan::IntervalTree; TIntervals = seqan::String, seqan::Alloc<> >]': +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:754:18: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:90:6: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 90 | itR = begin(ids); + | ~~~~^~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::buildAnnoCountStore(TAnnoCountStore&, seqan::FragmentStore&, TReadAnnoStore&) [with TAnnoCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:760:21: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:536:16: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 536 | itAnnoIds = begin(getValue(itRead).annoIds); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 205 | return TProxy(it); - | ^~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:537:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 537 | itAnnoIdsEnd = end(getValue(itRead).annoIds); + | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' - 88 | Proxy(TIterator const _it) - | ~~~~~~~~~~~~~~~~^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 94 | : data_iterator(_other.data_iterator) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h: In instantiation of 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:191:22: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 191 | itSecTuple = begin(tempSecTupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:192:25: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 192 | itSecTupleEnd = end(tempSecTupleSet); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:208:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 208 | itTuple = begin(tupleSet); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:209:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 209 | itTupleEnd = end(tupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:238:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 238 | itSecTuple = begin(secTupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:239:23: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 239 | itSecTupleEnd = end(secTupleSet); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:291:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 291 | itTuple = begin(tupleSet); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:292:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 292 | itTupleEnd = end(tupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:298:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 298 | itSecTuple = begin(secTupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:299:22: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 299 | itSecTupleEnd = end(secTupleSet); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::buildTupleCountStore(TTupleCountStore&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:624:22: required from 'void seqan::getResults(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:872:13: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:354:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 354 | itTuple = begin(tupleSet); + | ~~~~~~~~^~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:355:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 355 | itTupleEnd = end(tupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:384:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 384 | itSecTuple = begin(secTupleSet); + | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:385:23: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 385 | itSecTupleEnd = end(secTupleSet); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_journaled_set_solution_online_search_assignment2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/tutorial/journaled_set/solution_online_search_assignment2.cpp.o -o ../bin/demo_tutorial_journaled_set_solution_online_search_assignment2 -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -108126,113 +108610,49 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 89 | : data_iterator(_it) - | ^ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_journaled_set_solution_online_search_assignment2 +make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::String >, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:751:49: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ +Scanning dependencies of target mason_methylation +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Vcf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:873:31: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -108248,19 +108668,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' -/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bed_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:899:31: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); @@ -108276,27 +108694,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 95%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_assignment1 -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/tutorial/multiple_sequence_alignment/assignment1.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_assignment1 -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_multiple_sequence_alignment_assignment1 -make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend.internal". -Scanning dependencies of target fx_bam_coverage -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -108304,24 +108707,21 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -108334,7 +108734,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -108342,40 +108742,107 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h: In instantiation of 'void seqan::create_nTuple(TStringSet&, seqan::FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:122:60: required from 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:69:9: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 69 | itSet = begin(tempTupleSet); + | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:70:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 70 | itSetEnd = end(tempTupleSet); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h: In instantiation of 'void seqan::create_Tuple(TStringSet&, seqan::FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = unsigned int]': +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:126:41: required from 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:97:6: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 97 | it = begin(tempTupleSet); + | ~~~^~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: +/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:98:9: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] + 98 | itEnd = end(tempTupleSet); + | ~~~~~~^~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' + 105 | Iter(Iter const & other_) : + | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -108386,18 +108853,63 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -108430,113 +108942,161 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:848:15: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:330:27: required from 'int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:439:63: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_intervaltree.h:182:18: required from 'void seqan::findIntervalsForInterval(seqan::String&, TIntervalTree&, TInterval&, unsigned int) [with TIntervalTree = seqan::IntervalTree; TInterval = seqan::Interval; TCargo = unsigned int]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:85:27: required from 'void seqan::getIdsForRead(TAnnoIds&, seqan::FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TIntervalTree = seqan::IntervalTree; TIntervals = seqan::String, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:754:18: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1441 | act_prop = property(pm, act_knot); + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1453 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] + 1475 | next_prop = property(pm, targetVertex(it)); + | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' + 288 | IntervalTreeNode(IntervalTreeNode const & other) : + | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, @@ -108589,33 +109149,68 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:290:53: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:848:15: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_fastq_stats.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = unsigned int]': +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1618:57: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: @@ -108646,6 +109241,25 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1355:36: required from 'void doSnpAndMethCalling(TFragmentStore&, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, typename TFragmentStore::TContigPos, bool, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions; typename TFragmentStore::TContigPos = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:755:36: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: @@ -108677,39 +109291,112 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:248:12: required from 'bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:498:19: required from 'int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]' -/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:835:157: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 205 | return TProxy(it); + | ^~~~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:88:27: note: initializing argument 1 of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' + 88 | Proxy(TIterator const _it) + | ~~~~~~~~~~~~~~~~^~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(const seqan::Proxy >&) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:20: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:94:49: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 94 | : data_iterator(_other.data_iterator) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -108737,41 +109424,44 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:248:12: required from 'bool loadDatasets(TSequences&, const TFileNames&, TDatasets&) [with TSequences = seqan::StringSet, seqan::Owner<> >; TFileNames = std::vector >; TDatasets = seqan::String >]' +/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:498:19: required from 'int runDFI(const TFileNames&, TParamPredHull, TParamPred, bool, const DFIOptions&) [with TPredHull = PredMinFreq; TPred = PredMaxFreq; TAlphabet = unsigned char; TParamPredHull = seqan::String >; TParamPred = seqan::String >; TFileNames = std::vector >]' +/build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:835:157: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ @@ -108779,7 +109469,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ @@ -108787,317 +109477,236 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/fx_tools/fx_bam_coverage.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment5_solution -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment5_solution -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_parsing_command_line_arguments_assignment5_solution -make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend.internal". -Scanning dependencies of target gustaf_mate_joining -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp -[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example1_detailed -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/tutorial/parsing_command_line_arguments/example1_detailed.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example1_detailed -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example1_detailed -make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/depend.internal". -Scanning dependencies of target gustaf -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 95%] Building CXX object apps/gustaf/CMakeFiles/gustaf.dir/gustaf.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/gustaf.dir/gustaf.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp -[ 96%] Linking CXX executable ../bin/demo_unassigned_or_unused_bam_print_alignments -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/unassigned_or_unused/bam_print_alignments.cpp.o -o ../bin/demo_unassigned_or_unused_bam_print_alignments -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target demo_unassigned_or_unused_bam_print_alignments -make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/depend.internal". -Scanning dependencies of target insegt -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Building CXX object apps/insegt/CMakeFiles/insegt.dir/insegt.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.1.10\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/insegt.dir/insegt.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:28, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: + from /build/seqan2-2.4.0+dfsg/apps/dfi/dfi.cpp:26: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h: In instantiation of 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]': +/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:677:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 677 | Segment finderSegment(finderInfixSeq, + | ^~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' + 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:690:60: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, + | ^~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' + 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:17: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFasta_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' +/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:32: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:87, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, + from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h: In instantiation of 'seqan::Proxy >::Proxy(TIterator) [with TIterator = seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]': +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:205:12: required from 'typename seqan::Reference > > >::Type seqan::value(seqan::Iter > >&) [with TGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; typename seqan::Reference > > >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_base.h:250:17: required from 'typename seqan::Reference >::Type seqan::operator*(seqan::Iter&) [with TContainer = seqan::Gaps >, seqan::AnchorGaps > > >; TSpec = seqan::GapsIterator > > >; typename seqan::Reference >::Type = seqan::Proxy >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1628:55: required from 'void seqan::_printRead(TStream&, seqan::AlignedReadLayout&, TContigGaps&, TReadGaps&, TAlignedRead&, TLine) [with TStream = std::basic_ostream; TContigGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps >, seqan::AnchorGaps > > >; TAlignedRead = seqan::AlignedReadStoreElement, void>; TLine = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:1777:23: required from 'void seqan::printAlignment(TStream&, seqan::AlignedReadLayout&, seqan::FragmentStore&, TContigId, TPos, TPos, TNum, TNum) [with TStream = std::basic_ostream; TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigId = int; TPos = int; TNum = int]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.h:1163:31: required from 'void doCheckRealignCall(TFragmentStore&, TContigPos, TContigPos, TContigPos, TSetContigAnchorGaps&, TVcfStream&, TBedStream&, TMethOptions&, TOptions&) [with TFragmentStore = seqan::FragmentStore; TContigPos = int; TSetContigAnchorGaps = seqan::String >, seqan::Alloc<> >; TVcfStream = seqan::FormattedFile, seqan::Tag >; TBedStream = seqan::FormattedFile, seqan::Tag >; TMethOptions = MethCallingOptions; TOptions = SNPCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:742:35: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/proxy_iterator.h:89:32: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 89 | : data_iterator(_it) + | ^ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Embl_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:330:27: required from 'int _writeSequences(seqan::CharString&, const seqan::StringSet >&, const seqan::StringSet > >&, const seqan::StringSet > >&) [with TSequence = seqan::String, seqan::Alloc<> >; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:439:63: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::String, seqan::Alloc<> >; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps > > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner<> >]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = seqan::SnpStoreSpec_; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::String >, seqan::Alloc<> >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:751:49: required from 'bool detectSNPsForContig(seqan::VcfFileOut&, seqan::BedFileOut&, seqan::FragmentStore&, TContigId&, TBamFileIns&, TRecords&, TContigIntervals&, TOptions&, TMethOptions&) [with TSpec = seqan::SnpStoreSpec_; TContigId = int; TBamFileIns = std::vector, seqan::Tag >*>; TRecords = std::vector; TContigIntervals = seqan::String > >; TOptions = SNPCallingOptions; TMethOptions = MethCallingOptions; seqan::VcfFileOut = seqan::FormattedFile, seqan::Tag >; seqan::BedFileOut = seqan::FormattedFile, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:901:32: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 773 | Iter > > result = lhs; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] + 775 | return result; + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' + 112 | Iter const & operator = (Iter const & other_) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::GenBank_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:196:26: required from 'bool _importSequences(const CharString&, const CharString&, bool, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, seqan::String >&) [with TSequence = seqan::String, seqan::Alloc<> >; TId = seqan::String >; seqan::CharString = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:437:115: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:40: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/join_mates.cpp:41: + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h: In instantiation of 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]': -/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:677:33: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 677 | Segment finderSegment(finderInfixSeq, - | ^~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' - 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:27: -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:690:60: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 690 | Segment::Type, InfixSegment> patternSegment(patternInfixSeq, - | ^~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:102:46: note: initializing argument 1 of 'seqan::Segment::Segment(typename seqan::Parameter_ >::Type>::Type, typename seqan::Position >::Type>::Type, typename seqan::Position >::Type>::Type) [with THost_ = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Parameter_ >::Type>::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Position >::Type>::Type = unsigned int]' - 102 | Segment(typename Parameter_::Type _host, typename Position::Type _begin_index, typename Position::Type _end_index): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -109159,6 +109768,34 @@ | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Raw_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: recursively required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > > > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:996:18: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const seqan::StringSet > >&, bool) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig]' +/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io.h:1043:23: required from 'bool seqan::loadContigs(seqan::FragmentStore&, const TFileNames&) [with TFSSpec = seqan::SnpStoreSpec_; TFSConfig = seqan::FragmentStoreConfig; TFileNames = seqan::StringSet > >]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:792:16: required from 'int detectSNPs(SNPCallingOptions&, TMethOptions&) [with TMethOptions = MethCallingOptions]' +/build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:1265:49: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/apps/bs_tools/casbar.cpp:42: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:28, @@ -109185,89 +109822,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h: In instantiation of 'void seqan::createReadCountGFF(TFile&, TReadAnnoStore&, seqan::FragmentStore&) [with TFile = std::basic_fstream; TReadAnnoStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]': -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:889:23: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:75:14: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 75 | itAnnoIds = begin(getValue(itCountStore).annoIds); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:76:17: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 76 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:100:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 100 | itAnnoIds = begin(getValue(itCountStore).annoIds); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:101:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 101 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:134:16: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 134 | itAnnoIds = begin(getValue(itCountStore).annoIds); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:135:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 135 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:169:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 169 | itAnnoIds = begin(getValue(itCountStore).annoIds); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:20: -/build/seqan2-2.4.0+dfsg/apps/insegt/create_gff.h:170:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 170 | itAnnoIdsEnd = end(getValue(itCountStore).annoIds); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -109373,166 +109927,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:61, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:17: -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h: In instantiation of 'seqan::Iter > seqan::nodeDown(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]': -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:48:64: required from 'void seqan::adjustParentEntries(seqan::FragmentStore&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:851:21: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:853:50: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 853 | Iter > tmp(it); - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:855:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::AnnotationTree<> >::Iter(const seqan::Iter, seqan::AnnotationTree<> >&)' is deprecated [-Wdeprecated-copy] - 855 | return tmp; - | ^~~ -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_annotation.h:272:5: note: because 'seqan::Iter, seqan::AnnotationTree<> >' has user-provided 'const seqan::Iter >& seqan::Iter >::operator=(const seqan::Iter >&) [with TFragmentStore = seqan::FragmentStore<>; TSpec = void]' - 272 | operator = (Iter const &_origin) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::getIdsForRead(TAnnoIds&, seqan::FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TIntervalTree = seqan::IntervalTree; TIntervals = seqan::String, seqan::Alloc<> >]': -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:754:18: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:90:6: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 90 | itR = begin(ids); - | ~~~~^~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::buildAnnoCountStore(TAnnoCountStore&, seqan::FragmentStore&, TReadAnnoStore&) [with TAnnoCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:760:21: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:536:16: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 536 | itAnnoIds = begin(getValue(itRead).annoIds); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:537:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 537 | itAnnoIdsEnd = end(getValue(itRead).annoIds); - | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h: In instantiation of 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:191:22: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 191 | itSecTuple = begin(tempSecTupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:192:25: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 192 | itSecTupleEnd = end(tempSecTupleSet); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:208:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 208 | itTuple = begin(tupleSet); - | ~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:209:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 209 | itTupleEnd = end(tupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:238:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 238 | itSecTuple = begin(secTupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:239:23: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 239 | itSecTupleEnd = end(secTupleSet); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:291:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 291 | itTuple = begin(tupleSet); - | ~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:292:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 292 | itTupleEnd = end(tupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:298:19: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 298 | itSecTuple = begin(secTupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:21: -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:299:22: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 299 | itSecTupleEnd = end(secTupleSet); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': @@ -109550,50 +109944,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h: In instantiation of 'void seqan::buildTupleCountStore(TTupleCountStore&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]': -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:624:22: required from 'void seqan::getResults(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:872:13: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:354:15: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 354 | itTuple = begin(tupleSet); - | ~~~~~~~~^~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:355:18: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 355 | itTupleEnd = end(tupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:384:20: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 384 | itSecTuple = begin(secTupleSet); - | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:22: -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:385:23: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 385 | itSecTupleEnd = end(secTupleSet); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -109624,6 +109974,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_consensus +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/tutorial/multiple_sequence_alignment/consensus.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_consensus -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -109684,6 +110037,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_multiple_sequence_alignment_consensus +make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:190, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:52, from /build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:29, @@ -109745,6 +110105,12 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ +Scanning dependencies of target mason_frag_sequencing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/seeds.h:52, @@ -109803,29 +110169,6 @@ | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:46, from /build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:28, @@ -109854,56 +110197,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h: In instantiation of 'void seqan::create_nTuple(TStringSet&, seqan::FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:122:60: required from 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:69:9: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 69 | itSet = begin(tempTupleSet); - | ~~~~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:70:12: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 70 | itSetEnd = end(tempTupleSet); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h: In instantiation of 'void seqan::create_Tuple(TStringSet&, seqan::FragmentStore&, const TStringSet&, const TId&, const unsigned int&) [with TStringSet = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TId = unsigned int]': -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:126:41: required from 'void seqan::buildTupleCountStore_Fusion(TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, TReadAnnoStore&, unsigned int, bool) [with TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TReadAnnoStore = seqan::String >]' -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:761:29: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:97:6: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 97 | it = begin(tempTupleSet); - | ~~~^~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ -In file included from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:19: -/build/seqan2-2.4.0+dfsg/apps/insegt/base.h:98:9: warning: implicitly-declared 'constexpr seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >& seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >::operator=(const seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >&)' is deprecated [-Wdeprecated-copy] - 98 | itEnd = end(tempTupleSet); - | ~~~~~~^~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:74, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_position.h:105:5: note: because 'seqan::Iter >, seqan::Owner<> >, seqan::CountingIteratorImpl_ > >' has user-provided 'seqan::Iter > >::Iter(const seqan::Iter > >&) [with TContainer = seqan::StringSet >, seqan::Owner<> >]' - 105 | Iter(Iter const & other_) : - | ^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: @@ -109925,13 +110218,20 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_qgram_openaddressing.h:143:9: note: because 'seqan::Index, seqan::Alloc<> >, seqan::Dependent > >, seqan::IndexQGram, seqan::Tag > >' has user-provided 'seqan::Index > >::Index(const seqan::Index > >&) [with TObject = seqan::StringSet, seqan::Alloc<> >, seqan::Dependent > >; TShapeSpec = seqan::UngappedShape<0>]' 143 | Index(Index const &other): | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:50: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' /build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here @@ -109939,37 +110239,15 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGff_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:848:15: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:38: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:40: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -110003,22 +110281,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h: In instantiation of 'void seqan::findIntervals(seqan::String&, const seqan::Graph&, const TPropertyMap&, TValue) [with TSpec = seqan::Directed >; TPropertyMap = seqan::String, seqan::StorePointsOnly>, seqan::Alloc<> >; TValue = unsigned int; TCargo = unsigned int]': -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_intervaltree.h:182:18: required from 'void seqan::findIntervalsForInterval(seqan::String&, TIntervalTree&, TInterval&, unsigned int) [with TIntervalTree = seqan::IntervalTree; TInterval = seqan::Interval; TCargo = unsigned int]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:85:27: required from 'void seqan::getIdsForRead(TAnnoIds&, seqan::FragmentStore&, TIntervalTree&, TIntervals&, unsigned int) [with TAnnoIds = seqan::StringSet >, seqan::Owner<> >; TSpec = void; TConfig = seqan::FragmentStoreConfig; TIntervalTree = seqan::IntervalTree; TIntervals = seqan::String, seqan::Alloc<> >]' -/build/seqan2-2.4.0+dfsg/apps/insegt/fusion.h:754:18: required from 'void seqan::getResults_Fusion(TReadAnnoStore&, TAnnoCountStore&, TTupleCountStore&, TTupleCountStore_Fusion&, seqan::FragmentStore&, unsigned int, bool, unsigned int, unsigned int, bool) [with TReadAnnoStore = seqan::String >; TAnnoCountStore = seqan::String >; TTupleCountStore = seqan::String >; TTupleCountStore_Fusion = seqan::String >; TSpec = void; TConfig = seqan::FragmentStoreConfig]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:870:20: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1441:18: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1441 | act_prop = property(pm, act_knot); - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: @@ -110065,68 +110327,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/align/align_base.h:104:13: note: because 'seqan::Align, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>, seqan::Tag >' has user-provided 'seqan::Align& seqan::Align::operator=(const seqan::Align&) [with TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>, seqan::InfixSegment>; TSpec = seqan::Tag]' 104 | Align & operator=(Align const & other) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1453:23: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1453 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:1475:27: warning: implicitly-declared 'seqan::IntervalTreeNode, seqan::StorePointsOnly>& seqan::IntervalTreeNode, seqan::StorePointsOnly>::operator=(const seqan::IntervalTreeNode, seqan::StorePointsOnly>&)' is deprecated [-Wdeprecated-copy] - 1475 | next_prop = property(pm, targetVertex(it)); - | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:56, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/misc/interval_tree.h:288:5: note: because 'seqan::IntervalTreeNode, seqan::StorePointsOnly>' has user-provided 'seqan::IntervalTreeNode::IntervalTreeNode(const seqan::IntervalTreeNode&) [with TInterval = seqan::IntervalAndCargo]' - 288 | IntervalTreeNode(IntervalTreeNode const & other) : - | ^~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagGtf_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::True]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:257:14: required from 'seqan::FormattedFile::FormattedFile(const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:848:15: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:14: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: @@ -110170,206 +110370,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:697:26: required from 'bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:852:22: required from 'bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:697:26: required from 'bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:852:22: required from 'bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' -/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:90, - from /build/seqan2-2.4.0+dfsg/include/seqan/store.h:38, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:17: -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h: In instantiation of 'seqan::Iter > > seqan::operator+(const seqan::Iter > >&, TDifference) [with TGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors = seqan::String >; TDifference = long long int]': -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:679:35: required from 'typename seqan::Iterator >::Type seqan::iter(T&, TPos, const seqan::Tag&) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; TTag = seqan::Rooted_; typename seqan::Iterator >::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:661:16: required from 'typename seqan::Iterator::Type>::Type seqan::iter(T&, TPos) [with T = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TPos = long long int; typename seqan::Iterator::Type>::Type = seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_anchor.h:466:20: required from 'void seqan::insertGaps(seqan::Gaps >&, TPosition, TCount) [with TSequence = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapAnchors = seqan::String >; TPosition = long long int; TCount = long long int]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2236:27: required from 'void seqan::_alignedReadsInsertGaps(TAlignedReadIter, TAlignedReadIter, TPos, TSize, TReadSeqStore&) [with TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TPos = long long int; TSize = long long int; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2321:40: required from 'void seqan::_twoWayMergeAlignments(TContigGapsGlobal&, TContigGapsPW&, TReadGaps&, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TAlignedReadIter, TReadSeqStore&) [with TContigGapsGlobal = seqan::Gaps, seqan::AnchorGaps > > >; TContigGapsPW = seqan::Gaps, seqan::AnchorGaps >, seqan::InfixSegment> > >; TReadGaps = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TAlignedReadIter = seqan::AlignedReadStoreElement, void>*; TReadSeqStore = seqan::StringSet, seqan::Alloc<> >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2437:31: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:773:58: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 773 | Iter > > result = lhs; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:775:12: warning: implicitly-declared 'constexpr seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >::Iter(const seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >&)' is deprecated [-Wdeprecated-copy] - 775 | return result; - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/align/gaps_iterator_anchor.h:112:18: note: because 'seqan::Iter, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >, seqan::GapsIterator > > > >' has user-provided 'const seqan::Iter > >& seqan::Iter > >::operator=(const seqan::Iter > >&) [with TGaps_ = seqan::Gaps, seqan::Alloc<> >, seqan::InfixSegment>, seqan::AnchorGaps > > >; TGapAnchors_ = seqan::String >]' - 112 | Iter const & operator = (Iter const & other_) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment >, seqan::InfixSegment>*; TParam = const seqan::Segment >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TValue2 = const seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment >, seqan::InfixSegment>; TSource = seqan::Segment >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2393:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment >, seqan::InfixSegment>::Segment(const seqan::Segment >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:12: -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:548:19: required from 'typename seqan::Value::Type* seqan::_holderAllocateObject(THolder&, const TValue&) [with THolder = seqan::Holder, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Tag >; TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; typename seqan::Value::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:650:42: required from 'void seqan::create(seqan::Holder >&, TValue2&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TValue2 = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:887:15: required from 'void seqan::assignValue(seqan::Holder >&, const TSource&) [with TValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSource = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/holder_tristate.h:135:20: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_all.h:2394:29: required from 'void seqan::convertPairWiseToGlobalAlignment(seqan::FragmentStore&, TContigGapsString&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TContigGapsString = seqan::StringSet >, seqan::Owner > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:337:41: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::BamIOContext&, TForwardIter&, const TFormat&, const seqan::FragStoreImportFlags&) [with TSpec = void; TConfig = seqan::FragmentStoreConfig; TNameStore = seqan::StringSet > >; TNameStoreCache = seqan::NameStoreCache > > >; TStorageSpec = seqan::Dependent >; TForwardIter = seqan::Iter >, seqan::StreamIterator > >; TFormat = seqan::TagSelector, seqan::TagList > > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:361:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&, const seqan::FragStoreImportFlags&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/store/store_io_sam.h:373:16: required from 'void seqan::readRecords(seqan::FragmentStore&, seqan::FormattedFile, TDirection, TSpec>&) [with TFSSpec = void; TConfig = seqan::FragmentStoreConfig; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/insegt/overlap_module.h:839:16: required from 'bool seqan::ngsOverlapper(TOptions&) [with TOptions = InsegtOptions]' -/build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:199:26: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/insegt/insegt.cpp:13: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 96%] Linking CXX executable ../../bin/fx_fastq_stats -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_fastq_stats.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -o ../../bin/fx_fastq_stats -lrt -lz -lbz2 -[ 96%] Linking CXX executable ../../bin/four2three -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/four2three.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/four2three.dir/four2three.cpp.o -o ../../bin/four2three -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target fx_fastq_stats -make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/depend.internal". -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target four2three -make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/depend.internal". -Scanning dependencies of target mason_variator -Scanning dependencies of target mason_genome -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Building CXX object apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp -[ 96%] Building CXX object apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp -[ 96%] Linking CXX executable ../../bin/fx_bam_coverage -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_bam_coverage.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -o ../../bin/fx_bam_coverage -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 96%] Built target fx_bam_coverage -make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/depend.internal". -Scanning dependencies of target mason_methylation -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Building CXX object apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:50: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_genome.cpp:40: @@ -110412,16 +110412,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 96%] Linking CXX executable ../../bin/alf -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf && /usr/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/alf.dir/alf.cpp.o -o ../../bin/alf -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target alf -make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:45: @@ -110448,12 +110438,52 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -Scanning dependencies of target mason_frag_sequencing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Building CXX object apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_frag_sequencing.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1348:31: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:697:26: required from 'bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:852:22: required from 'bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:24: +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h: In instantiation of 'static void seqan::ValueConstructor_::construct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:305:28: required from 'void seqan::valueConstruct(TIterator, TParam&&) [with TIterator = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>*; TParam = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1354:27: required from 'static void seqan::AppendValueToString_::appendValue_(T&, TValue&&) [with T = seqan::String, seqan::Alloc<> >, seqan::InfixSegment>, seqan::Alloc<> >; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_base.h:1366:54: required from 'void seqan::appendValue(seqan::String&, TValue&&, seqan::Tag) [with TTargetValue = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TTargetSpec = seqan::Alloc<>; TValue = const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/string_set_owner.h:174:16: required from 'void seqan::appendValue(seqan::StringSet >&, const TString2&, seqan::Tag) [with TString = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TString2 = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TExpand = seqan::TagGenerous_]' +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/sequence_interface.h:937:16: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ] +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:697:26: required from 'bool _bestExtension(const TInfix&, const TInfix&, TSeed&, TSeed&, TPos, TPos, const TScore&, TDir, TSize, TEps, TAlign&) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSeed = seqan::Seed >; TPos = unsigned int; TDir = seqan::ExtensionDirection; TScore = seqan::Score >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar_extension.h:852:22: required from 'bool _extendAndExtract(const seqan::Align, seqan::InfixSegment> >&, TScoreValue, const TScore&, const seqan::Segment::Type, seqan::InfixSegment>&, const seqan::Segment::Type, seqan::InfixSegment>&, seqan::ExtensionDirection, TSize, TEps, TAlign&) [with TScoreValue = int; TScore = seqan::Score >; TSequence = seqan::String, seqan::Alloc<> >; TSize = int; TEps = double; TAlign = seqan::Align, seqan::Alloc<> >, seqan::Tag >; typename seqan::Infix::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:633:26: required from 'void verifySwiftHit(const seqan::Segment&, const seqan::Segment&, TEpsilon, TSize, TDrop, TDelta, TSize1, TSize1&, TSize1, TId&, bool, QueryMatches >&, TTag) [with TInfix = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TEpsilon = double; TSize = int; TDelta = unsigned int; TDrop = double; TSize1 = unsigned int; TId = seqan::String >; TSource = seqan::String, seqan::Alloc<> >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/../stellar/stellar.h:705:17: required from 'void stellar(seqan::Finder > >&, seqan::Pattern, TSpec>, seqan::Swift > >&, double, TSize, TDrop, TSize1, TSize1&, TSize1, TMode, TId&, bool, seqan::StringSet > >&, TTag) [with TText = seqan::String, seqan::Alloc<> >; TStringSetSpec = seqan::Dependent >; TIndexSpec = seqan::IndexQGram, seqan::Tag >; TSize = int; TDrop = double; TSize1 = unsigned int; TMode = bool; TSource = seqan::String, seqan::Alloc<> >; TId = seqan::String >; TTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/stellar_routines.h:197:20: required from 'void _getStellarMatches(seqan::StringSet >&, seqan::StringSet >&, seqan::StringSet > >&, StellarOptions&, TMatches&) [with TSequence = seqan::String, seqan::Alloc<> >; TMatches = seqan::StringSet, seqan::Alloc<> >, seqan::String > > > >]' +/build/seqan2-2.4.0+dfsg/apps/gustaf/msplazer_main.h:146:91: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/basic/array_construct_destruct.h:254:9: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 254 | new( (void*) & value(it) ) TNonConstValue(std::forward(param_)); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/gustaf/gustaf.cpp:25: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_variator.cpp:45: @@ -110624,6 +110654,38 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_assignment5_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/tutorial/parsing_command_line_arguments/assignment5_solution.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_assignment5_solution -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_parsing_command_line_arguments_assignment5_solution +make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/depend.internal". +Scanning dependencies of target mason_materializer +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Linking CXX executable ../bin/demo_tutorial_parsing_command_line_arguments_example1_detailed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/link.txt --verbose=1 +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/tutorial/parsing_command_line_arguments/example1_detailed.cpp.o -o ../bin/demo_tutorial_parsing_command_line_arguments_example1_detailed -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example1_detailed +make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/depend.internal". +Scanning dependencies of target mason_simulator +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 95%] Building CXX object apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp:39: @@ -110672,6 +110734,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 96%] Linking CXX executable ../bin/demo_unassigned_or_unused_bam_print_alignments +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/unassigned_or_unused/bam_print_alignments.cpp.o -o ../bin/demo_unassigned_or_unused_bam_print_alignments -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp:39: @@ -110739,6 +110804,13 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 96%] Built target demo_unassigned_or_unused_bam_print_alignments +make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/depend.internal". In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_methylation.cpp:39: @@ -110764,6 +110836,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +Scanning dependencies of target mason_tests +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 96%] Building CXX object apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp +[ 96%] Linking CXX executable ../bin/demo_tutorial_multiple_sequence_alignment_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos && /usr/bin/cmake -E cmake_link_script CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wno-unused-parameter -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/tutorial/multiple_sequence_alignment/assignment1.cpp.o -o ../bin/demo_tutorial_multiple_sequence_alignment_assignment1 -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 96%] Built target demo_tutorial_multiple_sequence_alignment_assignment1 +make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/depend.internal". +Scanning dependencies of target mason_splicing +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, @@ -110965,38 +111059,17 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 97%] Linking CXX executable ../../bin/gustaf_mate_joining -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf_mate_joining.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -o ../../bin/gustaf_mate_joining -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target gustaf_mate_joining -make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/depend.internal". -Scanning dependencies of target mason_materializer -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Building CXX object apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp -[ 97%] Linking CXX executable ../../bin/dfi -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi && /usr/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/dfi.dir/dfi.cpp.o -o ../../bin/dfi -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target dfi -make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/depend.internal". -Scanning dependencies of target mason_simulator -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Building CXX object apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, @@ -111009,11 +111082,39 @@ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' + 2048 | (_arg1), # _arg1, \ + | ^~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, + from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:38: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); + | ^~~~~~ +/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' + 2224 | (_arg1), # _arg1)) { \ + | ^~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ /build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] 320 | const_cast(indexText(me).data_begin) | ^ @@ -111102,6 +111203,18 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, + from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, + from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp:49: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_materializer.cpp:45: @@ -111130,6 +111243,33 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:52, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:52, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, @@ -111185,33 +111325,6 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:52, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:52, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/seq_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:52, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::TagFastq_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList, seqan::TagList > > > > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -111338,6 +111451,34 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_iterator.h:80, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:86, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -111415,6 +111556,35 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:82, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -111497,172 +111667,6 @@ 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' -/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:211:31: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' -/build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:228:96: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, - from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' - 143 | operator = (Segment const & source) - | ^~~~~~~~ -[ 97%] Linking CXX executable ../../bin/mason_genome -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../bin/mason_genome -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target mason_genome -make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/depend.internal". -Scanning dependencies of target mason_tests -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Building CXX object apps/mason2/CMakeFiles/mason_tests.dir/mason_tests.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_tests.dir/mason_tests.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp -[ 97%] Linking CXX executable ../../bin/bisar -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/bisar.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bisar.dir/bisar.cpp.o -o ../../bin/bisar -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target bisar -make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/depend.internal". -Scanning dependencies of target mason_splicing -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/mason2/CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/c++ -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp -[ 98%] Linking CXX executable ../../bin/insegt -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt && /usr/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/insegt.dir/insegt.cpp.o -o ../../bin/insegt -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:313:28: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 313 | SEQAN_ASSERT_EQ(sizeof(alph_t), 1); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2048:45: note: in definition of macro 'SEQAN_ASSERT_EQ' - 2048 | (_arg1), # _arg1, \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_debug.h:52, - from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:38: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:314:48: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 314 | SEQAN_ASSERT((IsSameType::Type, True>::VALUE)); - | ^~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/basic/debug_test_system.h:2224:44: note: in definition of macro 'SEQAN_ASSERT' - 2224 | (_arg1), # _arg1)) { \ - | ^~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target insegt -make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/depend.internal". -Scanning dependencies of target micro_razers -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:49, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_tests.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/bam_io.h:47, from /build/seqan2-2.4.0+dfsg/apps/mason2/sequencing.h:43, @@ -111685,18 +111689,28 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/apps/mason2/methylation_levels.h:38, - from /build/seqan2-2.4.0+dfsg/apps/mason2/genomic_variants.h:52, - from /build/seqan2-2.4.0+dfsg/apps/mason2/vcf_materialization.h:44, - from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp:49: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = seqan::String, seqan::Alloc<> >; TSpec = seqan::InfixSegment; typename seqan::Pointer_ >::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]': +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:117:40: required from 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' +/build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:586:12: required from 'seqan::Iter > seqan::operator+(const seqan::Iter >&, int) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:631:62: required from 'void seqan::_computeAlignmentImpl(TDPScout&, TDPScoreMatrixNavigator&, TDPTraceMatrixNavigator&, const TSequenceH&, const TSequenceV&, const TScoringScheme&, const TBand&, const seqan::DPProfile_&, const NavigateColumnWiseBanded&) [with TDPScout = seqan::DPScout_ >, seqan::If > >, seqan::Terminator_<>, seqan::Tag > >; TDPScoreMatrixNavigator = seqan::DPMatrixNavigator_ >, seqan::Tag, seqan::String >, seqan::Alloc<> > >, seqan::Tag, seqan::Tag >; TDPTraceMatrixNavigator = seqan::DPMatrixNavigator_, seqan::String >, seqan::DPTraceMatrix, seqan::Tag > > >, seqan::Tag >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoringScheme = seqan::Score >; TBand = seqan::DPBandConfig >; TAlignmentAlgo = seqan::GlobalAlignment_ >; TGapCosts = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; seqan::NavigateColumnWiseBanded = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_algorithm_impl.h:1417:26: required from 'typename seqan::Value::Type seqan::_computeAlignment(seqan::DPContext&, TTraceTarget&, TScoutState&, const TSequenceH&, const TSequenceV&, const TScoreScheme&, const seqan::DPBandConfig&, const seqan::DPProfile_&) [with TDPScoreValue = seqan::DPCell_ >; TTraceValue = unsigned char; TScoreMatHost = seqan::String >, seqan::Alloc<> >; TTraceMatHost = seqan::String; TTraceTarget = seqan::String >; TScoutState = seqan::DPScoutState_ >; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreScheme = seqan::Score >; TBandSwitch = seqan::Tag; TAlignmentAlgorithm = seqan::GlobalAlignment_ >; TGapScheme = seqan::Tag; TTraceFlag = seqan::TracebackOn, seqan::Tag > >; TExecPolicy = seqan::Tag; typename seqan::Value::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:287:29: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::DPContext, TTraceValue, TScoreMat, TTraceMat>&, seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&) [with TScoreValue = int; TGapSpec = seqan::Tag; TTraceValue = unsigned char; TScoreMat = seqan::String >, seqan::Alloc<> >; TTraceMat = seqan::String; TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/dp_setup.h:308:33: required from 'typename seqan::Value >::Type seqan::_setUpAndRunAlignment(seqan::String&, seqan::DPScoutState_&, const TSequenceH&, const TSequenceV&, const seqan::Score&, const seqan::AlignConfig2&, const TGapModel&) [with TTraceSegment = seqan::TraceSegment_; TSpec = seqan::Alloc<>; TDPScoutStateSpec = seqan::Tag; TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TSequenceV = seqan::String, seqan::Alloc<> >; TScoreValue2 = int; TScoreSpec = seqan::Tag; TDPType = seqan::GlobalAlignment_<>; TBand = seqan::DPBandConfig >; TFreeEndGaps = seqan::FreeEndGaps_; TTraceConfig = seqan::TracebackOn, seqan::Tag > >; TGapModel = seqan::Tag; typename seqan::Value >::Type = int]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:176:44: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int, const TAlgoTag&) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag; TAlgoTag = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/include/seqan/align/global_alignment_banded.h:211:31: required from 'TScoreValue seqan::globalAlignment(seqan::Gaps&, seqan::Gaps&, const seqan::Score&, const seqan::AlignConfig&, int, int) [with TSequenceH = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TGapsSpecH = seqan::Tag; TSequenceV = seqan::String, seqan::Alloc<> >; TGapsSpecV = seqan::Tag; TScoreValue = int; TScoreSpec = seqan::Tag; bool TOP = true; bool LEFT = false; bool RIGHT = false; bool BOTTOM = true; TACSpec = seqan::Tag]' +/build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:228:96: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>::Segment(const seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:96, + from /build/seqan2-2.4.0+dfsg/apps/mason2/fragment_generation.h:51, + from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_simulator.cpp:43: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' + 143 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, from /build/seqan2-2.4.0+dfsg/apps/mason2/mason_splicing.cpp:42: @@ -111913,6 +111927,86 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[ 97%] Linking CXX executable ../../bin/mason_tests +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../bin/mason_tests -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 +[ 97%] Linking CXX executable ../../bin/mason_genome +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_genome.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o ../../bin/mason_genome -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target mason_tests +make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/depend.internal". +Scanning dependencies of target micro_razers +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/micro_razers.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/micro_razers.dir/micro_razers.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target mason_genome +make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend.internal". +Scanning dependencies of target roi_feature_projection +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp +[ 97%] Linking CXX executable ../../bin/four2three +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/four2three.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/four2three.dir/four2three.cpp.o -o ../../bin/four2three -lrt -lz -lbz2 +[ 97%] Linking CXX executable ../../bin/fx_fastq_stats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_fastq_stats.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_fastq_stats.dir/fx_fastq_stats.cpp.o -o ../../bin/fx_fastq_stats -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target four2three +make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend.internal". +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target fx_fastq_stats +make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake --color= +Scanning dependencies of target bam2roi +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend.internal". +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp +Scanning dependencies of target roi_plot_thumbnails +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp +[ 97%] Linking CXX executable ../../bin/fx_bam_coverage +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/fx_bam_coverage.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/fx_bam_coverage.dir/fx_bam_coverage.cpp.o -o ../../bin/fx_bam_coverage -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target fx_bam_coverage +make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend.internal". +Scanning dependencies of target pair_align_lib +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build +make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/../razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp:37: @@ -111924,6 +112018,282 @@ 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:876:57: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:432:58: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:876:57: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +[ 98%] Linking CXX executable ../../bin/gustaf_mate_joining +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf_mate_joining.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf_mate_joining.dir/join_mates.cpp.o -o ../../bin/gustaf_mate_joining -lrt -lz -lbz2 +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:432:58: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 98%] Built target gustaf_mate_joining +[100%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, + from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.h:41, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:47: +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] + 320 | const_cast(indexText(me).data_begin) + | ^ +/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here + 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { + | ^~~~~~~~~~~ +[100%] Linking CXX executable ../../bin/alf +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf && /usr/bin/cmake -E cmake_link_script CMakeFiles/alf.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/alf.dir/alf.cpp.o -o ../../bin/alf -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[100%] Built target alf +[100%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, + from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/../razers/razers.h:28, @@ -111978,6 +112348,82 @@ 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:318:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, + from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, + from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/../razers/razers.h:28, @@ -112033,6 +112479,56 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 159 | TLowcase lowcaseFileName(fileName); + | ^~~~~~~~~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' + 150 | ModifiedString(typename Parameter_::Type host): + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': +/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:318:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] + 443 | return me; + | ^~ +In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, + from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: +/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' + 117 | operator = (Segment const & source) + | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:43, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/../razers/razers.h:28, @@ -112156,6 +112652,9 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ +[100%] Linking CXX executable ../../bin/mason_methylation +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../bin/mason_methylation -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/find.h:45, @@ -112184,9 +112683,6 @@ /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -[ 98%] Linking CXX executable ../../bin/mason_methylation -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_methylation.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o ../../bin/mason_methylation -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:222, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/../razers/razers.h:30, from /build/seqan2-2.4.0+dfsg/apps/micro_razers/micro_razers.cpp:37: @@ -112379,6 +112875,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/basic/iterator_adaptor.h:116:48: note: initializing argument 1 of 'seqan::Iter >::Iter(typename seqan::Parameter_::Type, TIterator) [with TContainer = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>; TIterator = seqan::SimpleType*; TSpec = seqan::Tag; typename seqan::Parameter_::Type = seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>]' 116 | Iter(typename Parameter_::Type container_, TIterator it_) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[100%] Built target mason_methylation +[100%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp In file included from /build/seqan2-2.4.0+dfsg/include/seqan/basic/basic_fundamental.h:72, from /build/seqan2-2.4.0+dfsg/include/seqan/basic.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:74, @@ -112606,61 +113106,10 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_infix.h:143:5: note: because 'seqan::Segment, seqan::Alloc<> >, seqan::InfixSegment>' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = seqan::String, seqan::Alloc<> >]' 143 | operator = (Segment const & source) | ^~~~~~~~ -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target mason_methylation -make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend.internal". -Scanning dependencies of target roi_feature_projection -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp -[ 98%] Linking CXX executable ../../bin/mason_tests -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_tests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_tests.dir/mason_tests.cpp.o -o ../../bin/mason_tests -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target mason_tests -make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/depend.internal". -Scanning dependencies of target bam2roi -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/bam2roi.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/bam2roi.dir/bam2roi.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:876:57: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -112670,21 +113119,25 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -112695,78 +113148,48 @@ 159 | TLowcase lowcaseFileName(fileName); | ^~~~~~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:46: + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: + from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:876:57: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_feature_projection.cpp:44: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, - from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.h:41, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:47: -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h: In function 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)': -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:320:30: warning: 'bool seqan::indexCreate(seqan::Index >&, PizzaChiliCompressed)' is deprecated: The PizzaChiliIndex is outdated and is not maintained anymore. [-Wdeprecated-declarations] - 320 | const_cast(indexText(me).data_begin) - | ^ -/build/seqan2-2.4.0+dfsg/include/seqan/index/index_pizzachili.h:307:1: note: declared here - 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { - | ^~~~~~~~~~~ -[ 98%] Linking CXX executable ../../bin/mason_frag_sequencing -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../bin/mason_frag_sequencing -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:318:60: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -112778,22 +113201,25 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -112806,84 +113232,86 @@ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:318:60: required from here +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' +/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' +/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] 443 | return me; | ^~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/bam2roi.cpp:40: + from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, + from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[ 98%] Linking CXX executable ../../bin/mason_variator -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../bin/mason_variator -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target mason_frag_sequencing -[ 98%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o +[100%] Linking CXX static library libpair_align_lib.a +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/cmake -P CMakeFiles/pair_align_lib.dir/cmake_clean_target.cmake +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align_lib.dir/link.txt --verbose=1 +/usr/bin/ar qc libpair_align_lib.a CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o +[100%] Building CXX object apps/ngs_roi/CMakeFiles/bam2roi.dir/roi_builder.cpp.o cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_builder.cpp -[ 98%] Linking CXX executable ../../bin/mason_materializer +[100%] Linking CXX executable ../../bin/mason_materializer cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_materializer.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o ../../bin/mason_materializer -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 +/usr/bin/ranlib libpair_align_lib.a make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target mason_variator -make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend.internal". -Scanning dependencies of target roi_plot_thumbnails +[100%] Built target mason_materializer +[100%] Linking CXX executable ../../bin/mason_frag_sequencing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_frag_sequencing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o ../../bin/mason_frag_sequencing -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp -[ 98%] Linking CXX executable ../../bin/casbar -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/casbar.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/casbar.dir/casbar.cpp.o -o ../../bin/casbar -lrt -lz -lbz2 +[100%] Built target mason_frag_sequencing +[100%] Linking CXX executable ../../bin/insegt +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt && /usr/bin/cmake -E cmake_link_script CMakeFiles/insegt.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/insegt.dir/insegt.cpp.o -o ../../bin/insegt -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target mason_materializer -make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend +[100%] Built target pair_align_lib +make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend.internal". -Scanning dependencies of target pair_align_lib +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake --color= +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/depend.internal". +Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/depend.internal". make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build +[100%] Built target insegt +Scanning dependencies of target pair_align +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Building CXX object apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp +[100%] Building CXX object apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align.dir/pair_align.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp +[100%] Linking CXX executable ../../bin/mason_variator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_variator.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o ../../bin/mason_variator -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target casbar -[100%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp +[100%] Built target mason_variator In file included from /build/seqan2-2.4.0+dfsg/include/seqan/index.h:194, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus/overlap_info_computation.h:38, from /build/seqan2-2.4.0+dfsg/include/seqan/consensus.h:65, @@ -112897,109 +113325,6 @@ 307 | indexCreate(Index >& me, PizzaChiliCompressed const) { | ^~~~~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:432:58: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Roi_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:432:58: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/arg_parse.h:46, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/roi_plot_thumbnails.cpp:41: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, @@ -113089,12 +113414,22 @@ /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ +[100%] Linking CXX executable ../../bin/mason_splicing +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../bin/mason_splicing -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 +[100%] Linking CXX executable ../../bin/dfi +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi && /usr/bin/cmake -E cmake_link_script CMakeFiles/dfi.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/dfi.dir/dfi.cpp.o -o ../../bin/dfi -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[100%] Built target dfi +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[100%] Built target mason_splicing In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' @@ -113107,42 +113442,14 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ @@ -113151,7 +113458,7 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' @@ -113165,74 +113472,22 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:47, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' 150 | ModifiedString(typename Parameter_::Type host): | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/gff_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.h:51, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_spliced.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': /build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' /build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' @@ -113247,240 +113502,55 @@ from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.cpp:37: + from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: /build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' 117 | operator = (Segment const & source) | ^~~~~~~~ -[100%] Linking CXX executable ../../bin/gustaf -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf.dir/gustaf.cpp.o -o ../../bin/gustaf -lrt -lz -lbz2 -[100%] Building CXX object apps/micro_razers/CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.0.11\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/razers/param_tabs.cpp -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target gustaf -[100%] Building CXX object apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/c++ -DSEQAN_APP_VERSION=\"0.2.12\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp [100%] Linking CXX executable ../../bin/mason_simulator cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_simulator.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o ../../bin/mason_simulator -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 -[100%] Linking CXX static library libpair_align_lib.a -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/cmake -P CMakeFiles/pair_align_lib.dir/cmake_clean_target.cmake -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align_lib.dir/link.txt --verbose=1 -/usr/bin/ar qc libpair_align_lib.a CMakeFiles/pair_align_lib.dir/pair_align_lib.cpp.o CMakeFiles/pair_align_lcs.dir/pair_align_lcs.cpp.o CMakeFiles/pair_align_local.dir/pair_align_local.cpp.o CMakeFiles/pair_align_global_0000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_0111.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1000.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1001.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1010.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1011.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1100.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1101.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1110.dir/pair_align_global.cpp.o CMakeFiles/pair_align_global_1111.dir/pair_align_global.cpp.o +[100%] Linking CXX executable ../../bin/roi_plot_thumbnails +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_plot_thumbnails.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -o ../../bin/roi_plot_thumbnails -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target mason_simulator -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:59, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/file.h:58, - from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:62, - from /build/seqan2-2.4.0+dfsg/include/seqan/bed_io.h:45, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.h:42, - from /build/seqan2-2.4.0+dfsg/apps/ngs_roi/project_interval.cpp:36: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -[100%] Linking CXX executable ../../bin/mason_splicing -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 && /usr/bin/cmake -E cmake_link_script CMakeFiles/mason_splicing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/mason_splicing.dir/mason_splicing.cpp.o -o ../../bin/mason_splicing -lrt -lz -lbz2 libmason_sim.a -lrt -lz -lbz2 +[100%] Built target roi_plot_thumbnails make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target mason_splicing +[100%] Built target mason_simulator [100%] Linking CXX executable ../../bin/roi_feature_projection cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_feature_projection.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_feature_projection.dir/roi_feature_projection.cpp.o CMakeFiles/roi_feature_projection.dir/project_spliced.cpp.o CMakeFiles/roi_feature_projection.dir/project_interval.cpp.o -o ../../bin/roi_feature_projection -lrt -lz -lbz2 -/usr/bin/ranlib libpair_align_lib.a make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [100%] Built target roi_feature_projection -[100%] Linking CXX executable ../../bin/roi_plot_thumbnails -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/roi_plot_thumbnails.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/roi_plot_thumbnails.dir/roi_plot_thumbnails.cpp.o -o ../../bin/roi_plot_thumbnails -lrt -lz -lbz2 +[100%] Linking CXX executable ../../bin/bisar +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/bisar.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bisar.dir/bisar.cpp.o -o ../../bin/bisar -lrt -lz -lbz2 [100%] Linking CXX executable ../../bin/bam2roi cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi && /usr/bin/cmake -E cmake_link_script CMakeFiles/bam2roi.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/bam2roi.dir/bam2roi.cpp.o CMakeFiles/bam2roi.dir/roi_builder.cpp.o -o ../../bin/bam2roi -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target roi_plot_thumbnails +[100%] Built target bisar make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [100%] Built target bam2roi +[100%] Linking CXX executable ../../bin/pair_align +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/pair_align.dir/pair_align.cpp.o -o ../../bin/pair_align lib/libpair_align_lib.a -lrt -lz -lbz2 +[100%] Linking CXX executable ../../bin/gustaf +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf && /usr/bin/cmake -E cmake_link_script CMakeFiles/gustaf.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/gustaf.dir/gustaf.cpp.o -o ../../bin/gustaf -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target pair_align_lib -make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake --color= -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/depend.internal". -Dependee "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender "/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/depend.internal". -Scanning dependencies of target pair_align +[100%] Built target gustaf make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build -make[4]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Building CXX object apps/pair_align/CMakeFiles/pair_align.dir/pair_align.cpp.o -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align && /usr/bin/c++ -DSEQAN_APP_VERSION=\"1.3.8\" -DSEQAN_DATE=\"\" -DSEQAN_DISABLE_VERSION_CHECK -DSEQAN_HAS_BZIP2=1 -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -I/build/seqan2-2.4.0+dfsg/include -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -o CMakeFiles/pair_align.dir/pair_align.cpp.o -c /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/stream.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/score.h:43, - from /build/seqan2-2.4.0+dfsg/include/seqan/graph_align.h:45, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:59, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h: In instantiation of 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Sam_]': -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:120:35: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 159 | TLowcase lowcaseFileName(fileName); - | ^~~~~~~~~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:75, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:150:53: note: initializing argument 1 of 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' - 150 | ModifiedString(typename Parameter_::Type host): - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:95, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h: In instantiation of 'typename seqan::Pointer_ >::Type seqan::_toPointer(seqan::Segment&) [with THost = const char*; TSpec = seqan::PrefixSegment; typename seqan::Pointer_ >::Type = seqan::Segment]': -/build/seqan2-2.4.0+dfsg/include/seqan/modifier/modifier_view.h:151:25: required from 'seqan::ModifiedString >::ModifiedString(typename seqan::Parameter_::Type) [with THost = const seqan::Segment; TFunctor = seqan::FunctorLowcase; typename seqan::Parameter_::Type = seqan::Segment]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:159:14: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::Tag) [with TFilename = seqan::Segment; TFormat_ = seqan::Bam_]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/guess_format.h:114:36: required from 'bool seqan::guessFormatFromFilename(const TFilename&, seqan::TagSelector&) [with TFilename = seqan::Segment; TTagList = seqan::TagList, seqan::TagList > >]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:722:37: required from 'bool seqan::_open(seqan::FormattedFile&, const char*, int, TThrowExceptions) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void; TThrowExceptions = seqan::False]' -/build/seqan2-2.4.0+dfsg/include/seqan/stream/formatted_file.h:739:17: required from 'bool seqan::open(seqan::FormattedFile&, const char*, int) [with TFileFormat = seqan::Tag; TDirection = seqan::Tag; TSpec = void]' -/build/seqan2-2.4.0+dfsg/include/seqan/bam_io/bam_index_bai.h:699:35: required from here -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_base.h:443:12: warning: implicitly-declared 'constexpr seqan::Segment::Segment(const seqan::Segment&)' is deprecated [-Wdeprecated-copy] - 443 | return me; - | ^~ -In file included from /build/seqan2-2.4.0+dfsg/include/seqan/sequence.h:98, - from /build/seqan2-2.4.0+dfsg/include/seqan/modifier.h:47, - from /build/seqan2-2.4.0+dfsg/include/seqan/align.h:57, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/lib/pair_align_lib.h:41, - from /build/seqan2-2.4.0+dfsg/apps/pair_align/pair_align.cpp:16: -/build/seqan2-2.4.0+dfsg/include/seqan/sequence/segment_prefix.h:117:5: note: because 'seqan::Segment' has user-provided 'seqan::Segment& seqan::Segment::operator=(const seqan::Segment&) [with THost_ = const char*]' - 117 | operator = (Segment const & source) - | ^~~~~~~~ +[100%] Built target pair_align +[100%] Linking CXX executable ../../bin/casbar +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools && /usr/bin/cmake -E cmake_link_script CMakeFiles/casbar.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -ffloat-store -ffp-contract=off -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/casbar.dir/casbar.cpp.o -o ../../bin/casbar -lrt -lz -lbz2 +make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[100%] Built target casbar [100%] Linking CXX executable ../../bin/micro_razers cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers && /usr/bin/cmake -E cmake_link_script CMakeFiles/micro_razers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/micro_razers.dir/micro_razers.cpp.o CMakeFiles/micro_razers.dir/__/razers/param_tabs.cpp.o -o ../../bin/micro_razers -lrt -lz -lbz2 make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [100%] Built target micro_razers -[100%] Linking CXX executable ../../bin/pair_align -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align && /usr/bin/cmake -E cmake_link_script CMakeFiles/pair_align.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/seqan2-2.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -W -Wall -pedantic -fopenmp -Wl,-z,relro -Wl,-z,now -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -rdynamic CMakeFiles/pair_align.dir/pair_align.cpp.o -o ../../bin/pair_align lib/libpair_align_lib.a -lrt -lz -lbz2 -make[4]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target pair_align make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[2]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' @@ -113491,7 +113561,7 @@ # cd manual && make html make[1]: Leaving directory '/build/seqan2-2.4.0+dfsg' dh_auto_build -Nseqan-apps - cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j18 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/seqan2-2.4.0+dfsg -B/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -113500,2108 +113570,2111 @@ make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/depend make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/DependInfo.cmake --color= make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles/seqan_library.dir/DependInfo.cmake --color= make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/depend make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/DependInfo.cmake --color= +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_local.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/seqan_library.dir/build.make CMakeFiles/seqan_library.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'CMakeFiles/seqan_library.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory 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apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0001.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build -[ 0%] Built target seqan_library make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1001.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1110.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake --color= -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lcs.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_local.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 0%] Built target pair_align_global_1111 -[ 0%] Built target pair_align_global_1110 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/DependInfo.cmake --color= -[ 0%] Built target pair_align_global_1100 -[ 0%] Built target pair_align_lcs -[ 0%] Built target pair_align_global_1001 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/depend -[ 1%] Built target pair_align_global_0001 -[ 1%] Built target pair_align_global_0000 -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/depend -[ 1%] Built target pair_align_local -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/depend -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/DependInfo.cmake --color= -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1111.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1100.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0000.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_sim.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0110.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1010.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0011.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build'. +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0010.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1101.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 1%] Built target pair_align_global_0010 -[ 1%] Built target pair_align_global_0110 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0100.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0101.dir/build'. +[ 0%] Built target seqan_library +[ 0%] Built target pair_align_global_1001 +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 1%] Built target pair_align_global_0001 +[ 1%] Built target pair_align_global_1110 +[ 1%] Built target pair_align_global_1111 +[ 1%] Built target pair_align_lcs +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build +[ 1%] Built target pair_align_local make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/depend make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/depend -[ 1%] Built target pair_align_global_1010 -[ 1%] Built target pair_align_global_0111 make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/depend -make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_sim.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/DependInfo.cmake --color= +[ 1%] Built target pair_align_global_1100 +make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/depend +make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend +[ 1%] Built target pair_align_global_0000 +[ 1%] Built target pair_align_global_1010 +make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend +[ 1%] Built target pair_align_global_0011 +make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend +make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend +[ 1%] Built target pair_align_global_0110 +make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_sim.dir/build.make apps/mason2/CMakeFiles/mason_sim.dir/build +make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/DependInfo.cmake --color= -[ 1%] Built target pair_align_global_0011 +make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend +[ 1%] Built target pair_align_global_0010 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1011.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' [ 2%] Built target pair_align_global_1101 -make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/depend -[ 2%] Built target pair_align_global_0100 -make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/depend -[ 2%] Built target pair_align_global_1011 +[ 2%] Built target pair_align_global_0101 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_do_search.dir/DependInfo.cmake --color= -make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/depend -make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/depend +make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/param_chooser/CMakeFiles/param_chooser.dir/DependInfo.cmake --color= -[ 2%] Built target pair_align_global_0101 -[ 3%] Built target mason_sim -make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/depend -make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/depend +make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_evaluate.dir/DependInfo.cmake --color= +make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend +[ 2%] Built target pair_align_global_0100 +make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rabema/CMakeFiles/rabema_prepare_sam.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers/CMakeFiles/razers.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_quality2prob.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3_simulate_reads.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build +[ 2%] Built target pair_align_global_1011 +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_do_search.dir/build.make apps/rabema/CMakeFiles/rabema_do_search.dir/build -make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make -f apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build.make apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/param_chooser/CMakeFiles/param_chooser.dir/build'. +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_0111.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build.make apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_do_search.dir/build'. +make -f apps/param_chooser/CMakeFiles/param_chooser.dir/build.make apps/param_chooser/CMakeFiles/param_chooser.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_evaluate.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build.make apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build'. +make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_do_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/rabema/CMakeFiles/rabema_evaluate.dir/build.make apps/rabema/CMakeFiles/rabema_evaluate.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_global_1000.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/razers/CMakeFiles/razers.dir/build.make apps/razers/CMakeFiles/razers.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_build_gold_standard.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/razers3/CMakeFiles/razers3_quality2prob.dir/build.make apps/razers3/CMakeFiles/razers3_quality2prob.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build'. +make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target pair_align_global_1000 +make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build +make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build +make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/razers/CMakeFiles/razers.dir/build'. +make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_prepare_sam.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target param_chooser make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_quality2prob.dir/build'. +make[3]: Nothing to be done for 'apps/rabema/CMakeFiles/rabema_evaluate.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 3%] Built target rabema_do_search -make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/depend -make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/depend -[ 3%] Built target rabema_evaluate -make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/depend -make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/depend -[ 3%] Built target rabema_build_gold_standard -[ 3%] Built target test_funcs_param_chooser -[ 3%] Built target rabema_prepare_sam -make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/depend -make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend -make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/rep_sep/CMakeFiles/rep_sep.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/razers3/CMakeFiles/razers3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sak/CMakeFiles/sak.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sam2matrix/CMakeFiles/sam2matrix.dir/DependInfo.cmake --color= -[ 3%] Built target razers3_simulate_reads -[ 4%] Built target razers -[ 4%] Built target razers3_quality2prob -make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/samcat/CMakeFiles/samcat.dir/DependInfo.cmake --color= -make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend -make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/rep_sep/CMakeFiles/rep_sep.dir/build.make apps/rep_sep/CMakeFiles/rep_sep.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/razers3/CMakeFiles/razers3.dir/build.make apps/razers3/CMakeFiles/razers3.dir/build +make[3]: Nothing to be done for 'apps/param_chooser/CMakeFiles/param_chooser.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/samcat/CMakeFiles/samcat.dir/build.make apps/samcat/CMakeFiles/samcat.dir/build -make -f apps/sak/CMakeFiles/sak.dir/build.make apps/sak/CMakeFiles/sak.dir/build +make -f apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build.make apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build +make -f apps/sam2matrix/CMakeFiles/sam2matrix.dir/build.make apps/sam2matrix/CMakeFiles/sam2matrix.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/sam2matrix/CMakeFiles/sam2matrix.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build +make[3]: Nothing to be done for 'apps/rep_sep/CMakeFiles/rep_sep.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/rep_sep/CMakeFiles/rep_sep.dir/build'. +make[3]: Nothing to be done for 'apps/param_chooser/CMakeFiles/test_funcs_param_chooser.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/sak/CMakeFiles/sak.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/samcat/CMakeFiles/samcat.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_search.dir/build'. +make[3]: Nothing to be done for 'apps/razers/CMakeFiles/razers.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_join.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_quality2prob.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_sim.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build -make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build'. +make[3]: Nothing to be done for 'apps/razers3/CMakeFiles/razers3_simulate_reads.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/sgip/CMakeFiles/sgip.dir/build'. +make[3]: Nothing to be done for 'apps/sam2matrix/CMakeFiles/sam2matrix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 4%] Built target sam2matrix -[ 4%] Built target rep_sep +make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/depend +[ 2%] Built target pair_align_global_1000 +[ 2%] Built target pair_align_global_0111 +[ 2%] Built target rabema_do_search +[ 2%] Built target rabema_prepare_sam +make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/depend +[ 2%] Built target test_funcs_param_chooser +make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/depend +[ 2%] Built target rabema_build_gold_standard +[ 2%] Built target param_chooser +[ 2%] Built target rabema_evaluate +[ 2%] Built target rep_sep +[ 3%] Built target razers +make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/depend +make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/depend +[ 3%] Built target razers3_quality2prob make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/depend -[ 4%] Built target samcat +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_join.dir/DependInfo.cmake --color= +[ 3%] Built target razers3 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/searchjoin/CMakeFiles/s4_search.dir/DependInfo.cmake --color= make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/depend -[ 4%] Built target s4_search +[ 3%] Built target sak +[ 3%] Built target samcat make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/depend -[ 4%] Built target sak -[ 4%] Built target s4_join -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build -make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend +[ 4%] Built target mason_sim make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/DependInfo.cmake --color= +make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/depend make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/depend -make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake --color= -[ 4%] Built target razers3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake --color= -[ 5%] Built target sgip +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/sgip/CMakeFiles/sgip.dir/DependInfo.cmake --color= +[ 4%] Built target razers3_simulate_reads +make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/depend make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/depend -[ 5%] Built target seqan_tcoffee make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/depend -make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/tree_recon/CMakeFiles/tree_recon.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/seqcons2/CMakeFiles/seqcons2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/snp_store/CMakeFiles/snp_store.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/seqcons2/CMakeFiles/seqcons2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/stellar/CMakeFiles/stellar.dir/DependInfo.cmake --color= +[ 4%] Built target sam2matrix +make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/depend +make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align/CMakeFiles/test_align.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_extend/CMakeFiles/test_align_extend.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build +make -f apps/searchjoin/CMakeFiles/s4_search.dir/build.make apps/searchjoin/CMakeFiles/s4_search.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build -make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/searchjoin/CMakeFiles/s4_join.dir/build.make apps/searchjoin/CMakeFiles/s4_join.dir/build +make -f apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build.make apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_search.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/sgip/CMakeFiles/sgip.dir/build.make apps/sgip/CMakeFiles/sgip.dir/build make -f tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build -[ 5%] Built target seqcons2 +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build -make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/tree_recon/CMakeFiles/tree_recon.dir/build.make apps/tree_recon/CMakeFiles/tree_recon.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/snp_store/CMakeFiles/snp_store.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/sgip/CMakeFiles/sgip.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/seqcons2/CMakeFiles/seqcons2.dir/build.make apps/seqcons2/CMakeFiles/seqcons2.dir/build +make -f apps/stellar/CMakeFiles/stellar.dir/build.make apps/stellar/CMakeFiles/stellar.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/searchjoin/CMakeFiles/s4_join.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/stellar/CMakeFiles/stellar.dir/build'. +make[3]: Nothing to be done for 'apps/seqan_tcoffee/CMakeFiles/seqan_tcoffee.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/snp_store/CMakeFiles/snp_store.dir/build.make apps/snp_store/CMakeFiles/snp_store.dir/build +make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_local_variable_length.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_local_equal_length.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/tree_recon/CMakeFiles/tree_recon.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'apps/stellar/CMakeFiles/stellar.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_global_variable_length.dir/build'. +make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/align/CMakeFiles/test_align.dir/build.make tests/align/CMakeFiles/test_align.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build.make tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/DependInfo.cmake --color= +make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build +make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/snp_store/CMakeFiles/snp_store.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 5%] Built target snp_store -[ 5%] Built target stellar -[ 6%] Built target test_align_simd_local_variable_length make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align_simd_global_equal_length.dir/build'. +make[3]: Nothing to be done for 'apps/seqcons2/CMakeFiles/seqcons2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 4%] Built target s4_search +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/align/CMakeFiles/test_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_extend/CMakeFiles/test_align_extend.dir/build.make tests/align_extend/CMakeFiles/test_align_extend.dir/build -[ 6%] Built target test_align_simd_local_equal_length -make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/depend -make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/depend -[ 6%] Built target test_align_simd_global_variable_length -make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/depend -make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/depend -make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/align_extend/CMakeFiles/test_align_extend.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 7%] Built target tree_recon -make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/DependInfo.cmake --color= -make -f tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/DependInfo.cmake --color= -[ 7%] Built target test_align make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake --color= -[ 7%] Built target test_align_simd_global_equal_length +make[3]: Nothing to be done for 'tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/depend +[ 4%] Built target s4_join +make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/depend +[ 4%] Built target seqan_tcoffee +[ 5%] Built target sgip +make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/depend +[ 6%] Built target test_align_simd_local_variable_length +[ 6%] Built target test_align_simd_local_equal_length +make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/depend make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/depend +[ 7%] Built target tree_recon +make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free/CMakeFiles/test_alignment_free.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_split/CMakeFiles/test_align_split.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/depend +[ 7%] Built target stellar make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/align_profile /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/align_profile/CMakeFiles/test_align_profile.dir/DependInfo.cmake --color= -make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align_parallel/CMakeFiles/test_align_parallel_interface.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 7%] Built target test_align_simd_global_variable_length make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/arg_parse/CMakeFiles/test_arg_parse.dir/DependInfo.cmake --color= -[ 7%] Built target test_align_extend -make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/depend +[ 7%] Built target test_align_simd_global_equal_length +make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/alignment_free/CMakeFiles/test_alignment_free.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_exception.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_concept.dir/build.make tests/basic/CMakeFiles/test_basic_concept.dir/depend +[ 7%] Built target seqcons2 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bam_io/CMakeFiles/test_bam_io.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_fundamental.dir/build.make tests/basic/CMakeFiles/test_basic_fundamental.dir/depend +[ 7%] Built target snp_store make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_exception.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_concept.dir/DependInfo.cmake --color= make -f tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 7%] Built target test_align +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_fundamental.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/depend +make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/depend +[ 7%] Built target test_align_extend [ 7%] Built target test_align_parallel_interface -make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/build +make -f tests/basic/CMakeFiles/test_basic_allocator.dir/build.make tests/basic/CMakeFiles/test_basic_allocator.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/build +make -f tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build.make tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_allocator.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/align_parallel/CMakeFiles/test_align_parallel_algorithm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_parallelism.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/align_parallel/CMakeFiles/test_align_parallel_data_structures.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align_split/CMakeFiles/test_align_split.dir/build'. +make -f tests/align_split/CMakeFiles/test_align_split.dir/build.make tests/align_split/CMakeFiles/test_align_split.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/align_profile/CMakeFiles/test_align_profile.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/DependInfo.cmake --color= +make -f tests/align_profile/CMakeFiles/test_align_profile.dir/build.make tests/align_profile/CMakeFiles/test_align_profile.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/build +make -f tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/alignment_free/CMakeFiles/test_alignment_free.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/arg_parse/CMakeFiles/test_arg_parse.dir/build.make tests/arg_parse/CMakeFiles/test_arg_parse.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/arg_parse/CMakeFiles/test_arg_parse.dir/build'. +make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/bam_io/CMakeFiles/test_bam_io.dir/build'. +make -f tests/alignment_free/CMakeFiles/test_alignment_free.dir/build.make tests/alignment_free/CMakeFiles/test_alignment_free.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/depend -[ 8%] Built target test_align_parallel_data_structures -[ 8%] Built target test_align_split -make -f tests/basic/CMakeFiles/test_basic_concept.dir/build.make tests/basic/CMakeFiles/test_basic_concept.dir/depend -make -f tests/basic/CMakeFiles/test_basic_fundamental.dir/build.make tests/basic/CMakeFiles/test_basic_fundamental.dir/depend -[ 8%] Built target test_alignment_free -[ 8%] Built target test_align_parallel_algorithm make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_exception.dir/build.make tests/basic/CMakeFiles/test_basic_exception.dir/build -[ 8%] Built target test_align_profile -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_metaprogramming.dir/DependInfo.cmake --color= -make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/depend -make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/depend -make -f tests/basic/CMakeFiles/test_basic_allocator.dir/build.make tests/basic/CMakeFiles/test_basic_allocator.dir/depend +make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_exception.dir/build'. +make[3]: Nothing to be done for 'tests/align_split/CMakeFiles/test_align_split.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 8%] Built target test_bam_io -[ 8%] Built target test_arg_parse -[ 8%] Built target test_arg_parse_version_check -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_fundamental.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_alphabet.dir/DependInfo.cmake --color= -make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/depend -make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_concept.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_aggregate.dir/DependInfo.cmake --color= -make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_allocator.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_proxy.dir/DependInfo.cmake --color= +make -f tests/bam_io/CMakeFiles/test_bam_io.dir/build.make tests/bam_io/CMakeFiles/test_bam_io.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_parallelism.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/arg_parse/CMakeFiles/test_arg_parse_version_check.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_math.dir/DependInfo.cmake --color= -[ 8%] Built target test_basic_exception +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_exception.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build.make tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build -make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_metaprogramming.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/arg_parse/CMakeFiles/test_arg_parse.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_fundamental.dir/build.make tests/basic/CMakeFiles/test_basic_fundamental.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake --color= make -f tests/basic/CMakeFiles/test_basic_concept.dir/build.make tests/basic/CMakeFiles/test_basic_concept.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_alphabet.dir/build'. +make[3]: Nothing to be done for 'tests/align_profile/CMakeFiles/test_align_profile.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_fundamental.dir/build.make tests/basic/CMakeFiles/test_basic_fundamental.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_alphabet.dir/build.make tests/basic/CMakeFiles/test_basic_alphabet.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_concept.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_fundamental.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 7%] Built target test_align_parallel_algorithm make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_concept.dir/build'. +make[3]: Nothing to be done for 'tests/alignment_free/CMakeFiles/test_alignment_free.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_allocator.dir/build.make tests/basic/CMakeFiles/test_basic_allocator.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/bam_io/CMakeFiles/test_bam_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_aggregate.dir/build'. +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_alphabet.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_allocator.dir/build.make tests/basic/CMakeFiles/test_basic_allocator.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_aggregate.dir/build.make tests/basic/CMakeFiles/test_basic_aggregate.dir/build make -f tests/basic/CMakeFiles/test_basic_proxy.dir/build.make tests/basic/CMakeFiles/test_basic_proxy.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_allocator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_parallelism.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/basic/CMakeFiles/test_basic_parallelism.dir/build.make tests/basic/CMakeFiles/test_basic_parallelism.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_proxy.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_parallelism.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_math.dir/build.make tests/basic/CMakeFiles/test_basic_math.dir/build -[ 8%] Built target test_basic_metaprogramming make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_math.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_aggregate.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 8%] Built target test_align_parallel_data_structures +[ 8%] Built target test_align_split +make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/depend +[ 8%] Built target test_align_profile +[ 8%] Built target test_arg_parse_version_check make -f tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build.make tests/basic/CMakeFiles/test_basic_smart_pointer.dir/depend -[ 8%] Built target test_basic_alphabet -[ 8%] Built target test_basic_concept make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/depend -[ 9%] Built target test_basic_fundamental -[ 9%] Built target test_basic_parallelism +[ 8%] Built target test_arg_parse +[ 8%] Built target test_basic_exception make -f tests/bed_io/CMakeFiles/test_bed_io.dir/build.make tests/bed_io/CMakeFiles/test_bed_io.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_smart_pointer.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_iterator.dir/DependInfo.cmake --color= +[ 8%] Built target test_alignment_free +make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/depend +[ 8%] Built target test_bam_io +[ 8%] Built target test_basic_metaprogramming make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_container.dir/DependInfo.cmake --color= -make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/build -[ 10%] Built target test_basic_aggregate -[ 11%] Built target test_basic_proxy -[ 11%] Built target test_basic_allocator -make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/depend -make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_iterator.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/basic/CMakeFiles/test_basic_smart_pointer.dir/DependInfo.cmake --color= +make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/depend +[ 8%] Built target test_basic_concept make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/depend -[ 11%] Built target test_basic_math +[ 9%] Built target test_basic_fundamental +make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/bed_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/bed_io/CMakeFiles/test_bed_io.dir/DependInfo.cmake --color= -make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/depend -make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/depend -make -f tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build.make tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/depend +[ 9%] Built target test_basic_alphabet make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/blast /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/blast/CMakeFiles/test_blast.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake --color= +[ 9%] Built target test_basic_allocator +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/find/CMakeFiles/test_find.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake --color= +make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/depend +[ 10%] Built target test_basic_aggregate +[ 10%] Built target test_basic_math +make -f tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build.make tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/depend +[ 11%] Built target test_basic_parallelism +[ 11%] Built target test_basic_proxy +make -f tests/graph_align/CMakeFiles/test_graph_align.dir/build.make tests/graph_align/CMakeFiles/test_graph_align.dir/depend +make -f tests/graph_msa/CMakeFiles/test_graph_msa.dir/build.make tests/graph_msa/CMakeFiles/test_graph_msa.dir/depend +make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/gff_io/CMakeFiles/test_gff_io.dir/DependInfo.cmake --color= +make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_algorithms /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/DependInfo.cmake --color= -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus/CMakeFiles/test_consensus.dir/DependInfo.cmake --color= +make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/DependInfo.cmake --color= -[ 11%] Built target test_basic_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake --color= +make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align/CMakeFiles/test_graph_align.dir/DependInfo.cmake --color= +make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_msa /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa/CMakeFiles/test_graph_msa.dir/DependInfo.cmake --color= +make -f tests/index/CMakeFiles/test_index_swift.dir/build.make tests/index/CMakeFiles/test_index_swift.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/build -make -f tests/graph_align/CMakeFiles/test_graph_align.dir/build.make tests/graph_align/CMakeFiles/test_graph_align.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_container.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_swift.dir/DependInfo.cmake --color= +make -f tests/basic/CMakeFiles/test_basic_iterator.dir/build.make tests/basic/CMakeFiles/test_basic_iterator.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build.make tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build +make -f tests/basic/CMakeFiles/test_basic_container.dir/build.make tests/basic/CMakeFiles/test_basic_container.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/bed_io/CMakeFiles/test_bed_io.dir/build.make tests/bed_io/CMakeFiles/test_bed_io.dir/build +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_iterator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_align/CMakeFiles/test_graph_align.dir/DependInfo.cmake --color= -make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/bed_io/CMakeFiles/test_bed_io.dir/build'. +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_smart_pointer.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/blast/CMakeFiles/test_blast.dir/build'. +make -f tests/bed_io/CMakeFiles/test_bed_io.dir/build.make tests/bed_io/CMakeFiles/test_bed_io.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/find/CMakeFiles/test_find.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/basic/CMakeFiles/test_basic_container.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/blast/CMakeFiles/test_blast.dir/build.make tests/blast/CMakeFiles/test_blast.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/consensus/CMakeFiles/test_consensus.dir/build.make tests/consensus/CMakeFiles/test_consensus.dir/build +make -f tests/find/CMakeFiles/test_find.dir/build.make tests/find/CMakeFiles/test_find.dir/build make -f tests/gff_io/CMakeFiles/test_gff_io.dir/build.make tests/gff_io/CMakeFiles/test_gff_io.dir/build -[ 11%] Built target test_basic_container +make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build.make tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build -make -f tests/graph_msa/CMakeFiles/test_graph_msa.dir/build.make tests/graph_msa/CMakeFiles/test_graph_msa.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/gff_io/CMakeFiles/test_gff_io.dir/build'. +make[3]: Nothing to be done for 'tests/bed_io/CMakeFiles/test_bed_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_msa/CMakeFiles/test_graph_msa.dir/build.make tests/graph_msa/CMakeFiles/test_graph_msa.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/consensus/CMakeFiles/test_consensus.dir/build'. +make[3]: Nothing to be done for 'tests/gff_io/CMakeFiles/test_gff_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build'. +make[3]: Nothing to be done for 'tests/find/CMakeFiles/test_find.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 11%] Built target test_basic_smart_pointer make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build'. +make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_types.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_msa /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_msa/CMakeFiles/test_graph_msa.dir/DependInfo.cmake --color= -[ 11%] Built target test_bed_io -[ 11%] Built target test_blast +make[3]: Nothing to be done for 'tests/blast/CMakeFiles/test_blast.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build.make tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build make -f tests/graph_align/CMakeFiles/test_graph_align.dir/build.make tests/graph_align/CMakeFiles/test_graph_align.dir/build -make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/depend -[ 11%] Built target test_find -make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_utils.dir/DependInfo.cmake --color= -make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/depend -[ 11%] Built target test_consensus +make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_align/CMakeFiles/test_graph_align.dir/build'. +make[3]: Nothing to be done for 'tests/consensus/CMakeFiles/test_consensus.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_gff_io -make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_types.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_index_swift.dir/build.make tests/index/CMakeFiles/test_index_swift.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_derived.dir/DependInfo.cmake --color= -[ 12%] Built target test_graph_algorithms -make -f tests/index/CMakeFiles/test_index_repeats.dir/build.make tests/index/CMakeFiles/test_index_repeats.dir/depend -[ 12%] Built target test_consensus_v2 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_swift.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_msa/CMakeFiles/test_graph_msa.dir/build.make tests/graph_msa/CMakeFiles/test_graph_msa.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_repeats.dir/DependInfo.cmake --color= -[ 12%] Built target test_graph_align make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/graph_msa/CMakeFiles/test_graph_msa.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build -make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_finder.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build'. +make[3]: Nothing to be done for 'tests/graph_algorithms/CMakeFiles/test_graph_algorithms.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_types.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_types.dir/build +make -f tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build make -f tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_swift.dir/build.make tests/index/CMakeFiles/test_index_swift.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_types.dir/build'. +make[3]: Nothing to be done for 'tests/consensus_v2/CMakeFiles/test_consensus_v2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_utils.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_iterators.dir/build'. +make[3]: Nothing to be done for 'tests/graph_align/CMakeFiles/test_graph_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_derived.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_msa -make -f tests/index/CMakeFiles/test_index_swift.dir/build.make tests/index/CMakeFiles/test_index_swift.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_repeats.dir/build.make tests/index/CMakeFiles/test_index_repeats.dir/build -make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_swift.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build.make tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_repeats.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/graph_types/CMakeFiles/test_graph_types_property_map.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 12%] Built target test_graph_types_utils -make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/build -make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/depend +[ 11%] Built target test_basic_iterator +make -f tests/index/CMakeFiles/test_index_repeats.dir/build.make tests/index/CMakeFiles/test_index_repeats.dir/depend +[ 11%] Built target test_basic_container +[ 11%] Built target test_basic_smart_pointer +[ 11%] Built target test_graph_algorithms +[ 11%] Built target test_bed_io +[ 11%] Built target test_blast +[ 11%] Built target test_consensus +[ 12%] Built target test_gff_io +[ 12%] Built target test_find make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake --color= -[ 12%] Built target test_graph_types_iterators +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_repeats.dir/DependInfo.cmake --color= [ 12%] Built target test_graph_types_types -[ 12%] Built target test_graph_types_derived +[ 12%] Built target test_graph_msa +make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/depend +make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/depend +make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/depend +make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/depend +[ 12%] Built target test_graph_align +[ 12%] Built target test_consensus_v2 make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_finder.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_graph_types_property_map -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake --color= -[ 13%] Built target test_index_swift +[ 12%] Built target test_graph_types_iterators make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/depend make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/depend -make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/build make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/depend +make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake --color= -[ 13%] Built target test_index_repeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_view.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_vstree.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_view.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_finder.dir/DependInfo.cmake --color= +make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_bifm.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_qgram.dir/DependInfo.cmake --color= +[ 12%] Built target test_graph_types_utils +[ 12%] Built target test_graph_types_derived +make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend +[ 12%] Built target test_index_swift +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend +make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/depend +make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/depend +[ 13%] Built target test_graph_types_property_map make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/build -[ 13%] Built target test_index_finder -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_vstree.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_index_view -make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/build -make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/build +make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_bifm.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake --color= +make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_qgram.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake --color= +make -f tests/index/CMakeFiles/test_index_repeats.dir/build.make tests/index/CMakeFiles/test_index_repeats.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_repeats.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_vstree.dir/build.make tests/index/CMakeFiles/test_index_vstree.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build -[ 13%] Built target test_index_vstree +make -f tests/index/CMakeFiles/test_index_finder.dir/build.make tests/index/CMakeFiles/test_index_finder.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_view.dir/build.make tests/index/CMakeFiles/test_index_view.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/index/CMakeFiles/test_index_crosscompare_char.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char.dir/build +make -f tests/index/CMakeFiles/test_index_bifm.dir/build.make tests/index/CMakeFiles/test_index_bifm.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_vstree.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_qgram.dir/build.make tests/index/CMakeFiles/test_index_qgram.dir/build +make -f tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build make -f tests/index/CMakeFiles/test_index_base.dir/build.make tests/index/CMakeFiles/test_index_base.dir/build -make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/build -make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_finder.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_char.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_char_dfi.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm.dir/build.make tests/index/CMakeFiles/test_index_fm.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_base.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_view.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 13%] Built target test_index_bifm +make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_char.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_bifm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/depend -make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build -[ 13%] Built target test_index_crosscompare_char_dfi -make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build.make tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build make -f tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build.make tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/DependInfo.cmake --color= -[ 13%] Built target test_index_qgram -[ 13%] Built target test_index_fm_rank_dictionary -[ 15%] Built target test_index_crosscompare_char -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_qgram.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 13%] Built target test_index_repeats make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/depend -[ 15%] Built target test_index_base -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_shapes.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/depend -[ 16%] Built target test_index_fm -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_creation.dir/DependInfo.cmake --color= -make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/depend -make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend -make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find2_index_approx.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_drawing.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake --color= -[ 16%] Built target test_index_crosscompare_dna -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_base.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm_rank_dictionary.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/index/CMakeFiles/test_index_shapes.dir/build.make tests/index/CMakeFiles/test_index_shapes.dir/build -[ 16%] Built target test_index_crosscompare_dna_dfi +make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake --color= -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_dna.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build -make -f tests/index/CMakeFiles/test_index_creation.dir/build.make tests/index/CMakeFiles/test_index_creation.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_shapes.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_crosscompare_dna_dfi.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/index/CMakeFiles/test_index_drawing.dir/build.make tests/index/CMakeFiles/test_index_drawing.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_creation.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_shapes.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_creation.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/build +[ 13%] Built target test_index_vstree +[ 13%] Built target test_index_finder +make -f tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build.make tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_drawing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_find2_index_approx.dir/build.make tests/index/CMakeFiles/test_find2_index_approx.dir/build +make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/depend +[ 13%] Built target test_index_crosscompare_char_dfi +[ 13%] Built target test_index_view +[ 13%] Built target test_index_bifm +[ 15%] Built target test_index_crosscompare_char +make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_find2_index_approx.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/journaled_set/CMakeFiles/test_journaled_set.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build'. +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_sa_bwtwalk.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_find_backtracking.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 17%] Built target test_index_shapes -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build -[ 17%] Built target test_index_creation +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_find_backtracking.dir/DependInfo.cmake --color= +[ 15%] Built target test_index_base +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/depend +[ 15%] Built target test_index_qgram +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/depend +[ 16%] Built target test_index_fm +[ 16%] Built target test_index_crosscompare_dna +[ 16%] Built target test_index_crosscompare_dna_dfi +[ 16%] Built target test_index_fm_rank_dictionary make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/depend make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 17%] Built target test_index_sa_bwtwalk -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 17%] Built target test_index_drawing -[ 17%] Built target test_journaled_set +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/index/CMakeFiles/test_index_fm_sparse_string.dir/DependInfo.cmake --color= make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/depend -[ 17%] Built target test_find2_index_approx make -f tests/map/CMakeFiles/test_map.dir/build.make tests/map/CMakeFiles/test_map.dir/depend make -f tests/misc/CMakeFiles/test_misc.dir/build.make tests/misc/CMakeFiles/test_misc.dir/depend -make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_set/CMakeFiles/test_journaled_set.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/DependInfo.cmake --color= -[ 17%] Built target test_find_backtracking -[ 17%] Built target test_index_fm_sparse_string -make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/map /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/map/CMakeFiles/test_map.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/misc /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/misc/CMakeFiles/test_misc.dir/DependInfo.cmake --color= +make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/DependInfo.cmake --color= +[ 16%] Built target test_index_drawing +[ 17%] Built target test_index_shapes +[ 17%] Built target test_index_creation +make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/depend +make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier/CMakeFiles/test_modifier.dir/DependInfo.cmake --color= -make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/depend -[ 18%] Built target test_journaled_string_tree_find -[ 18%] Built target test_journaled_string_tree_traverser -make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/depend +[ 17%] Built target test_index_sa_bwtwalk make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/modifier_cyclic_shape /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/DependInfo.cmake --color= +make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/depend +[ 17%] Built target test_find2_index_approx +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_find_backtracking.dir/build.make tests/index/CMakeFiles/test_find_backtracking.dir/build make -f tests/parse_lm/CMakeFiles/test_parse_lm.dir/build.make tests/parse_lm/CMakeFiles/test_parse_lm.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parallel/CMakeFiles/test_parallel.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build.make tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/parse_lm /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/parse_lm/CMakeFiles/test_parse_lm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build'. +make -f tests/journaled_set/CMakeFiles/test_journaled_set.dir/build.make tests/journaled_set/CMakeFiles/test_journaled_set.dir/build +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_find_backtracking.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/misc/CMakeFiles/test_misc.dir/build.make tests/misc/CMakeFiles/test_misc.dir/build +make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/depend +make -f tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build.make tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build make -f tests/map/CMakeFiles/test_map.dir/build.make tests/map/CMakeFiles/test_map.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build +make -f tests/misc/CMakeFiles/test_misc.dir/build.make tests/misc/CMakeFiles/test_misc.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build'. +make[3]: Nothing to be done for 'tests/journaled_set/CMakeFiles/test_journaled_set.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/index/CMakeFiles/test_index_fm_sparse_string.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build.make tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build.make tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/DependInfo.cmake --color= +make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/map/CMakeFiles/test_map.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_delta_map.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/misc/CMakeFiles/test_misc.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/map/CMakeFiles/test_map.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_find.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/modifier/CMakeFiles/test_modifier.dir/build'. +make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree_traverser.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_journaled_string_tree.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/journaled_string_tree/CMakeFiles/test_basic_observable.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/modifier/CMakeFiles/test_modifier.dir/build.make tests/modifier/CMakeFiles/test_modifier.dir/build +make -f tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build.make tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/parallel/CMakeFiles/test_parallel.dir/build.make tests/parallel/CMakeFiles/test_parallel.dir/build +[ 17%] Built target test_find_backtracking make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build'. +make[3]: Nothing to be done for 'tests/modifier/CMakeFiles/test_modifier.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/parallel/CMakeFiles/test_parallel.dir/build'. +make[3]: Nothing to be done for 'tests/modifier_cyclic_shape/CMakeFiles/test_modifier_cyclic_shape.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 18%] Built target test_journaled_string_tree make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/parse_lm/CMakeFiles/test_parse_lm.dir/build.make tests/parse_lm/CMakeFiles/test_parse_lm.dir/build -make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/depend -[ 19%] Built target test_delta_map -[ 19%] Built target test_misc make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/parse_lm/CMakeFiles/test_parse_lm.dir/build'. +make[3]: Nothing to be done for 'tests/parallel/CMakeFiles/test_parallel.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 19%] Built target test_map -make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/depend +make -f tests/parse_lm/CMakeFiles/test_parse_lm.dir/build.make tests/parse_lm/CMakeFiles/test_parse_lm.dir/build +[ 17%] Built target test_journaled_set make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/depend +[ 17%] Built target test_index_fm_sparse_string make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/pipe/CMakeFiles/test_pipe.dir/DependInfo.cmake --color= -[ 19%] Built target test_basic_observable -[ 19%] Built target test_modifier make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build.make tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/platform/CMakeFiles/test_platform.dir/DependInfo.cmake --color= -make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/depend -[ 19%] Built target test_modifier_cyclic_shape +make[3]: Nothing to be done for 'tests/parse_lm/CMakeFiles/test_parse_lm.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/random/CMakeFiles/test_random.dir/DependInfo.cmake --color= -[ 19%] Built target test_parallel -make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/depend -make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 18%] Built target test_delta_map +make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/build +make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/depend +[ 18%] Built target test_map make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/realign/CMakeFiles/test_realign.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/DependInfo.cmake --color= -[ 19%] Built target test_parse_lm -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/pipe/CMakeFiles/test_pipe.dir/build.make tests/pipe/CMakeFiles/test_pipe.dir/build +[ 19%] Built target test_journaled_string_tree_find +make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/depend +make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/platform/CMakeFiles/test_platform.dir/build.make tests/platform/CMakeFiles/test_platform.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/platform/CMakeFiles/test_platform.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/pipe/CMakeFiles/test_pipe.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/random/CMakeFiles/test_random.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/realign/CMakeFiles/test_realign.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Built target test_multiple_translation_units -make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/rna_io/CMakeFiles/test_rna_io.dir/DependInfo.cmake --color= +[ 19%] Built target test_journaled_string_tree_traverser make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build'. +make[3]: Nothing to be done for 'tests/platform/CMakeFiles/test_platform.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 19%] Built target test_misc +[ 19%] Built target test_journaled_string_tree +make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/rna_io/CMakeFiles/test_rna_io.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/score/CMakeFiles/test_score.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/score/CMakeFiles/test_score.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/roi_io/CMakeFiles/test_roi_io.dir/DependInfo.cmake --color= +[ 19%] Built target test_modifier +[ 19%] Built target test_basic_observable +[ 19%] Built target test_modifier_cyclic_shape make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/depend -[ 20%] Built target test_platform -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/roi_io/CMakeFiles/test_roi_io.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 20%] Built target test_pipe +[ 19%] Built target test_parallel make -f tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_base.dir/depend make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake --color= -[ 20%] Built target test_reduced_aminoacid -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_base.dir/DependInfo.cmake --color= -[ 20%] Built target test_random make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/depend -[ 20%] Built target test_score make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/depend -[ 20%] Built target test_rna_io -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake --color= -[ 21%] Built target test_realign make -f tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build.make tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_combination.dir/build'. +make[3]: Nothing to be done for 'tests/multiple_translation_units/CMakeFiles/test_multiple_translation_units.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_combination.dir/DependInfo.cmake --color= +[ 19%] Built target test_parse_lm make -f tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_base.dir/DependInfo.cmake --color= make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/depend -[ 21%] Built target test_roi_io make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_extension.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/DependInfo.cmake --color= -make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/random/CMakeFiles/test_random.dir/build.make tests/random/CMakeFiles/test_random.dir/build +[ 19%] Built target test_pipe make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/DependInfo.cmake --color= +[ 19%] Built target test_platform +make -f tests/realign/CMakeFiles/test_realign.dir/build.make tests/realign/CMakeFiles/test_realign.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/random/CMakeFiles/test_random.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_seeds_combination -make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build.make tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build +make -f tests/roi_io/CMakeFiles/test_roi_io.dir/build.make tests/roi_io/CMakeFiles/test_roi_io.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/rna_io/CMakeFiles/test_rna_io.dir/build.make tests/rna_io/CMakeFiles/test_rna_io.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/score/CMakeFiles/test_score.dir/build.make tests/score/CMakeFiles/test_score.dir/build +[ 20%] Built target test_multiple_translation_units make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build'. +make[3]: Nothing to be done for 'tests/roi_io/CMakeFiles/test_roi_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build -make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_extension.dir/build'. +make[3]: Nothing to be done for 'tests/reduced_aminoacid/CMakeFiles/test_reduced_aminoacid.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build'. +make[3]: Nothing to be done for 'tests/score/CMakeFiles/test_score.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_combination.dir/build.make tests/seeds/CMakeFiles/test_seeds_combination.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/realign/CMakeFiles/test_realign.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/rna_io/CMakeFiles/test_rna_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build -make -f tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_extension.dir/build.make tests/seeds/CMakeFiles/test_seeds_extension.dir/build +make -f tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build make -f tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build.make tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_set_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build'. +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_combination.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build.make tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build'. +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_chained.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build +make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build'. +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_extension.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_seeds_seed_base +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build.make tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build -[ 21%] Built target test_seeds_extension make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build'. +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_set_unordered.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/depend -make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_global_chaining.dir/build'. +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_banded_chain_alignment_interface.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 21%] Built target test_seeds_seed_set_base -[ 21%] Built target test_seeds_seed_chained -[ 21%] Built target test_seeds_seed_set_unordered +make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_seed_diagonal.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/DependInfo.cmake --color= +[ 20%] Built target test_random +[ 20%] Built target test_reduced_aminoacid +make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/seq_io/CMakeFiles/test_seq_io.dir/DependInfo.cmake --color= +[ 20%] Built target test_roi_io +[ 21%] Built target test_realign +make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/depend make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/depend make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/depend -make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_stringset_v2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence_v2.dir/DependInfo.cmake --color= -[ 23%] Built target test_seeds_banded_chain_alignment_interface -[ 23%] Built target test_seeds_seed_diagonal -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Built target test_seeds_align_banded_chain_impl +make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence/CMakeFiles/test_sequence.dir/DependInfo.cmake --color= -make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake --color= -make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend +[ 21%] Built target test_rna_io make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/DependInfo.cmake --color= +[ 21%] Built target test_score +[ 21%] Built target test_seeds_combination +[ 21%] Built target test_seeds_seed_set_base +make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/depend +[ 21%] Built target test_seeds_global_chaining make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/depend -make -f tests/store/CMakeFiles/test_store.dir/build.make tests/store/CMakeFiles/test_store.dir/depend -[ 23%] Built target test_seeds_global_chaining +[ 21%] Built target test_seeds_seed_chained make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/seq_io/CMakeFiles/test_seq_io.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simd/CMakeFiles/test_simd_vector.dir/DependInfo.cmake --color= +make -f tests/store/CMakeFiles/test_store.dir/build.make tests/store/CMakeFiles/test_store.dir/depend +[ 21%] Built target test_seeds_extension +[ 21%] Built target test_seeds_seed_base +[ 21%] Built target test_seeds_seed_set_unordered make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/DependInfo.cmake --color= make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/depend +make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/depend +[ 22%] Built target test_seeds_banded_chain_alignment_interface +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake --color= +make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend +[ 23%] Built target test_seeds_seed_diagonal +make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/depend +make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/store/CMakeFiles/test_store.dir/DependInfo.cmake --color= +make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/statistics/CMakeFiles/test_statistics.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/stream/CMakeFiles/test_stream.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake --color= +make -f tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build.make tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/sequence/CMakeFiles/test_stringset_v2.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/sequence/CMakeFiles/test_sequence_v2.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake --color= +make -f tests/seq_io/CMakeFiles/test_seq_io.dir/build.make tests/seq_io/CMakeFiles/test_seq_io.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 23%] Built target test_seq_io make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/sequence/CMakeFiles/test_stringset_v2.dir/build.make tests/sequence/CMakeFiles/test_stringset_v2.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/seeds/CMakeFiles/test_seeds_align_banded_chain_impl.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build make -f tests/sequence/CMakeFiles/test_sequence.dir/build.make tests/sequence/CMakeFiles/test_sequence.dir/build -make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/build +make -f tests/sequence/CMakeFiles/test_sequence_v2.dir/build.make tests/sequence/CMakeFiles/test_sequence_v2.dir/build +make -f tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build.make tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build'. +make[3]: Nothing to be done for 'tests/sequence/CMakeFiles/test_stringset_v2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/simd/CMakeFiles/test_simd_vector.dir/build.make tests/simd/CMakeFiles/test_simd_vector.dir/build make -f tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build.make tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/sequence/CMakeFiles/test_sequence.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/simd/CMakeFiles/test_simd_vector.dir/build'. +make[3]: Nothing to be done for 'tests/sequence/CMakeFiles/test_sequence_v2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/seq_io/CMakeFiles/test_seq_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/store/CMakeFiles/test_store.dir/build.make tests/store/CMakeFiles/test_store.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build'. +make[3]: Nothing to be done for 'tests/sequence_journaled/CMakeFiles/test_sequence_journaled.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/store/CMakeFiles/test_store.dir/build'. +make[3]: Nothing to be done for 'tests/simd/CMakeFiles/test_simd_vector.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/simple_intervals_io/CMakeFiles/test_simple_intervals_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 24%] Built target test_stringset_v2 -[ 25%] Built target test_sequence_v2 -make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/build -make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/depend -make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f tests/stream/CMakeFiles/test_stream.dir/build.make tests/stream/CMakeFiles/test_stream.dir/build -[ 25%] Built target test_sequence_journaled -make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/depend -[ 25%] Built target test_sequence -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/statistics/CMakeFiles/test_statistics.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/tabix_io/CMakeFiles/test_tabix_io.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/stream/CMakeFiles/test_stream.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/swift_local/CMakeFiles/test_find_swift.dir/DependInfo.cmake --color= -[ 25%] Built target test_simple_intervals_io -[ 25%] Built target test_simd_vector -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/translation/CMakeFiles/test_translation.dir/DependInfo.cmake --color= -make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/DependInfo.cmake --color= -[ 25%] Built target test_store -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/tests/vcf_io/CMakeFiles/test_vcf_io.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/DependInfo.cmake --color= -[ 25%] Built target test_stream +make -f tests/statistics/CMakeFiles/test_statistics.dir/build.make tests/statistics/CMakeFiles/test_statistics.dir/build +make -f tests/store/CMakeFiles/test_store.dir/build.make tests/store/CMakeFiles/test_store.dir/build +make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/build make -f tests/swift_local/CMakeFiles/test_find_swift.dir/build.make tests/swift_local/CMakeFiles/test_find_swift.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/stream/CMakeFiles/test_stream.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_statistics -make -f tests/translation/CMakeFiles/test_translation.dir/build.make tests/translation/CMakeFiles/test_translation.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/tabix_io/CMakeFiles/test_tabix_io.dir/build.make tests/tabix_io/CMakeFiles/test_tabix_io.dir/build +make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/translation/CMakeFiles/test_translation.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'tests/tabix_io/CMakeFiles/test_tabix_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/swift_local/CMakeFiles/test_find_swift.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'tests/store/CMakeFiles/test_store.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build.make tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'tests/statistics/CMakeFiles/test_statistics.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f tests/vcf_io/CMakeFiles/test_vcf_io.dir/build.make tests/vcf_io/CMakeFiles/test_vcf_io.dir/build +make[3]: Nothing to be done for 'tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/ucsc_io/CMakeFiles/test_ucsc_io.dir/build'. +make[3]: Nothing to be done for 'tests/vcf_io/CMakeFiles/test_vcf_io.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'tests/vcf_io/CMakeFiles/test_vcf_io.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 23%] Built target test_seeds_align_banded_chain_impl make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution2.dir/build'. +make[3]: Nothing to be done for 'tests/swift_local/CMakeFiles/test_find_swift.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_tabix_io -[ 25%] Built target test_translation -[ 25%] Built target test_find_swift +[ 24%] Built target test_stringset_v2 +[ 24%] Built target test_sequence +[ 24%] Built target test_seq_io +[ 25%] Built target test_sequence_v2 +[ 25%] Built target test_simd_vector +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/depend +[ 25%] Built target test_simple_intervals_io +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/depend make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/depend make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/depend make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build +[ 25%] Built target test_sequence_journaled make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/DependInfo.cmake --color= +[ 25%] Built target test_statistics make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target test_vcf_io +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/DependInfo.cmake --color= -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution2 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/DependInfo.cmake --color= +[ 25%] Built target test_stream make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution3 -[ 25%] Built target test_ucsc_io +[ 25%] Built target test_translation make -f demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/depend +[ 25%] Built target test_store make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/DependInfo.cmake --color= +[ 25%] Built target test_tabix_io make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake --color= +[ 25%] Built target test_find_swift +[ 25%] Built target test_ucsc_io +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution3 +[ 25%] Built target test_vcf_io +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution2 +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/DependInfo.cmake --color= -[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/depend -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution1 -make -f demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build -[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_solution1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_replace_as.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_reader_demo.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build -[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_reader_demo -make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build -[ 25%] Built target demo_unassigned_or_unused_tutorial_file_io_solution1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_replace_as -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/depend -[ 25%] Built target demo_unassigned_or_unused_modifier_modview -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build make -f demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_rooted_iterator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/DependInfo.cmake --color= -[ 25%] Built target demo_unassigned_or_unused_modifier_nested -[ 25%] Built target demo_unassigned_or_unused_rooted_iterator -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_nested.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 25%] Built target demo_unassigned_or_unused_modifier_modreverse -make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend -[ 25%] Built target demo_unassigned_or_unused_sam2svg -make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_modview.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_modifier_modreverse.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake --color= -[ 25%] Built target demo_unassigned_or_unused_minimapper -[ 26%] Built target demo_unassigned_or_unused_index_supermaxrepeats +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_sam2svg.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_sufarray.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_supermaxrepeats.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build +[ 25%] Built target demo_unassigned_or_unused_tutorial_file_io_solution1 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_minimapper.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_lcp.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_find_stringset.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_find.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_index_find_stringset -[ 27%] Built target demo_unassigned_or_unused_index_sufarray -make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/DependInfo.cmake --color= +[ 25%] Built target demo_unassigned_or_unused_tutorials_custim_io_reader_demo +[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_all_strings +[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_sequence_iterator_demo +[ 25%] Built target demo_unassigned_or_unused_tutorial_sequence_replace_as +[ 25%] Built target demo_unassigned_or_unused_sam2svg +[ 25%] Built target demo_unassigned_or_unused_rooted_iterator +[ 25%] Built target demo_unassigned_or_unused_modifier_nested +[ 25%] Built target demo_unassigned_or_unused_modifier_modview +make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/depend +[ 25%] Built target demo_unassigned_or_unused_modifier_modreverse +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/depend make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 26%] Built target demo_unassigned_or_unused_index_supermaxrepeats +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build +[ 26%] Built target demo_unassigned_or_unused_minimapper +make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend +make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend +[ 26%] Built target demo_unassigned_or_unused_index_sufarray +[ 27%] Built target demo_unassigned_or_unused_index_find_stringset +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend [ 27%] Built target demo_unassigned_or_unused_index_lcp +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_graph_hmm_silent -[ 27%] Built target demo_unassigned_or_unused_index_find -make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/depend +make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake --color= +[ 27%] Built target demo_unassigned_or_unused_index_find +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_find_wild -make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build -[ 27%] Built target demo_unassigned_or_unused_filter_sam make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/depend -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_graph_hmm_silent.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build -[ 27%] Built target demo_unassigned_or_unused_soft_to_hard_masking -make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_file_format -make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_bam_library_size.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_base.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build'. +make -f demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build.make demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_find_wild.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build -[ 27%] Built target demo_unassigned_or_unused_bamutil make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_bamutil.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_unassigned_or_unused_bam_library_size +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_filter_sam.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_soft_to_hard_masking.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/DependInfo.cmake --color= -[ 27%] Built target demo_unassigned_or_unused_arg_align +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_file_format.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_arg_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build -make -f demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_solution2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_example_iterators.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 27%] Built target demo_tutorial_workflows_knime_node -[ 29%] Built target demo_tutorial_vcf_io_solution3 -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/depend -[ 29%] Built target demo_unassigned_or_unused_annotation_converter -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/depend -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/depend -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_workflows_knime_node.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 27%] Built target demo_unassigned_or_unused_graph_hmm_silent make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_annotation_converter.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_3_workshop_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake --color= -[ 29%] Built target demo_tutorial_vcf_io_solution2 -[ 29%] Built target demo_tutorial_string_sets_base +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_example_iterators -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build +[ 27%] Built target demo_unassigned_or_unused_find_wild +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/depend +[ 27%] Built target demo_unassigned_or_unused_bam_library_size +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/depend +[ 27%] Built target demo_unassigned_or_unused_filter_sam +[ 27%] Built target demo_unassigned_or_unused_soft_to_hard_masking +[ 27%] Built target demo_unassigned_or_unused_file_format +[ 27%] Built target demo_unassigned_or_unused_bamutil +[ 29%] Built target demo_tutorial_vcf_io_solution3 +[ 29%] Built target demo_unassigned_or_unused_arg_align +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/depend +[ 29%] Built target demo_unassigned_or_unused_annotation_converter +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/depend make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_2_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_tutorial_vcf_io_solution2 make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/depend +[ 29%] Built target demo_tutorial_string_sets_example_iterators make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/depend +[ 29%] Built target demo_tutorial_workflows_knime_node make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/DependInfo.cmake --color= [ 29%] Built target demo_tutorial_string_sets_assignment_3_workshop_solution -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build +[ 29%] Built target demo_tutorial_string_sets_base +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_1_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/depend +[ 29%] Built target demo_tutorial_string_sets_assignment_1_solution +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 29%] Built target demo_tutorial_string_sets_assignment_2_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 29%] Built target demo_tutorial_string_sets_assignment_2_solution -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/DependInfo.cmake --color= -[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_solution2 -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build -[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_assignment5 -[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_assignment4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_assignment2 -[ 30%] Built target demo_tutorial_string_sets_assignment_1_solution make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build make -f demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 30%] Built target demo_tutorial_sequences_in_depth_example_overflow -[ 30%] Built target demo_tutorial_sequences_in_depth_base -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_example_overflow.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 30%] Built target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/DependInfo.cmake --color= -[ 30%] Built target demo_unassigned_or_unused_index_mums -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Built target demo_tutorial_sequences_example_functionality2 +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_in_depth_assignment_exact_generous_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_6_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_mums.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_3_solution.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_5_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_functionality1.dir/build'. +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_conversions_move.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_functionality2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build -[ 31%] Built target demo_tutorial_sequences_example_conversions_move -[ 31%] Built target demo_tutorial_sequences_example_functionality1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build +[ 29%] Built target demo_tutorial_simple_rna_seq_genequant_assignment5 +[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_solution2 +[ 30%] Built target demo_tutorial_sequences_in_depth_assignment_exact_generous_solution +make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build +[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_assignment4 +make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_characters.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 31%] Built target demo_tutorial_sequences_assignment_3_solution +[ 30%] Built target demo_tutorial_sequences_in_depth_example_overflow +[ 30%] Built target demo_tutorial_sequences_in_depth_base +[ 30%] Built target demo_unassigned_or_unused_index_mums +[ 30%] Built target demo_tutorial_simple_rna_seq_genequant_assignment2 +[ 30%] Built target demo_tutorial_sequences_assignment_3_solution +[ 31%] Built target demo_tutorial_sequences_assignment_6_solution +[ 31%] Built target demo_tutorial_sequences_example_functionality1 +[ 31%] Built target demo_tutorial_sequences_assignment_5_solution +[ 32%] Built target demo_tutorial_sequences_example_functionality2 +[ 32%] Built target demo_tutorial_sequences_example_conversions_move +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/depend +[ 33%] Built target demo_unassigned_or_unused_tutorial_sequence_count_characters make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/depend -[ 32%] Built target demo_tutorial_sequences_assignment_6_solution -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend -[ 32%] Built target demo_tutorial_sequences_assignment_5_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/depend +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_example1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 33%] Built target demo_tutorial_sequences_assignment_1_solution -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend +[ 34%] Built target demo_tutorial_sequences_assignment_1_solution +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/depend -[ 34%] Built target demo_unassigned_or_unused_tutorial_sequence_count_characters +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/DependInfo.cmake --color= -[ 34%] Built target demo_tutorial_sequence_io_solution2 -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/depend -[ 35%] Built target demo_tutorial_sequence_io_example1 -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build -[ 35%] Built target demo_tutorial_sequence_io_base -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake --color= +[ 34%] Built target demo_tutorial_sequence_io_solution2 +[ 35%] Built target demo_tutorial_sequence_io_example1 +make -f demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_4_workshop_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_seeds_solution1 -[ 35%] Built target demo_tutorial_seed_and_extend_solution6 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_seed_and_extend_example6 -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/depend -[ 35%] Built target demo_tutorial_seed_and_extend_solution2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 35%] Built target demo_tutorial_string_sets_assignment_4_workshop_solution -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/depend -[ 35%] Built target demo_tutorial_seed_and_extend_example7 -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream_write.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/DependInfo.cmake --color= -[ 35%] Built target demo_unassigned_or_unused_benchmark_stream_write -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/DependInfo.cmake --color= -[ 36%] Built target demo_tutorial_seed_and_extend_example5 -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend -[ 36%] Built target demo_tutorial_seed_and_extend_example2 -[ 36%] Built target demo_tutorial_seed_and_extend_example4 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution6.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seeds_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example6.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram_hash.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_exact.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_index_multiple.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build -[ 36%] Built target demo_tutorial_q_gram_index_index_qgram_hash -make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example7.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment6.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_tutorial_q_gram_index_index_assignment5 -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example4.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build'. -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_assignment5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build +[ 35%] Built target demo_tutorial_sequence_io_base +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/depend +[ 35%] Built target demo_tutorial_seed_and_extend_solution6 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_seeds.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 36%] Built target demo_unassigned_or_unused_seeds -[ 36%] Built target demo_tutorial_q_gram_index_index_assignment6 +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/depend +[ 35%] Built target demo_tutorial_seed_and_extend_solution2 +[ 35%] Built target demo_tutorial_string_sets_assignment_4_workshop_solution +[ 35%] Built target demo_tutorial_seeds_solution1 +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/depend +[ 35%] Built target demo_tutorial_seed_and_extend_example6 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/DependInfo.cmake --color= +[ 36%] Built target demo_tutorial_seed_and_extend_example5 +[ 36%] Built target demo_unassigned_or_unused_benchmark_stream_write +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/depend +[ 36%] Built target demo_tutorial_seed_and_extend_example2 +[ 36%] Built target demo_tutorial_q_gram_index_index_qgram_hash +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/depend +[ 36%] Built target demo_tutorial_seed_and_extend_example7 make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/depend +[ 36%] Built target demo_tutorial_seed_and_extend_example4 make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/depend -[ 36%] Built target demo_tutorial_pattern_matching_find_exact -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake --color= -[ 37%] Built target demo_tutorial_pattern_matching_find_index_multiple make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/depend +[ 36%] Built target demo_tutorial_q_gram_index_index_assignment6 +[ 37%] Built target demo_tutorial_pattern_matching_find_index_multiple +make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend +[ 37%] Built target demo_tutorial_pattern_matching_find_exact make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/DependInfo.cmake --color= -[ 37%] Built target demo_tutorial_alignment_scoring_scheme_simple make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/DependInfo.cmake --color= +[ 37%] Built target demo_tutorial_q_gram_index_index_assignment5 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/depend -[ 37%] Built target demo_dox_index_UNUSED_shape_hash -[ 37%] Built target demo_tutorial_alphabets_assignment_1 -[ 37%] Built target demo_tutorial_a_first_example_solution_5 -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/depend -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/depend +[ 37%] Built target demo_unassigned_or_unused_seeds +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build make -f demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build.make demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build make -f demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build +make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_assignment_1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_file_readwrite.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_simple.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_kruskals_algorithm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_3.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_realignment_step2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_filter_similar_sequences.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build.make demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build -[ 37%] Built target demo_tutorial_a_first_example_solution_3 make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_begin_range_goDown_representative_repLength.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_qgram_counts.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_4_solution.dir/build'. @@ -115609,2981 +115682,2978 @@ make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 37%] Built target demo_howto_filter_similar_sequences -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_own_function.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/depend -[ 38%] Built target demo_tutorial_realignment_step2 -[ 38%] Built target demo_unassigned_or_unused_file_readwrite -make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_dox_index_UNUSED_shape_hash +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/depend +[ 37%] Built target demo_tutorial_alignment_scoring_scheme_simple make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/DependInfo.cmake --color= -[ 38%] Built target demo_dox_graph_algorithms_kruskals_algorithm -[ 38%] Built target demo_unassigned_or_unused_index_qgram_counts -[ 38%] Built target demo_dox_index_begin_range_goDown_representative_repLength +[ 37%] Built target demo_tutorial_alphabets_assignment_1 +make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/depend -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/depend -make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/depend -[ 38%] Built target demo_tutorial_genome_annotations_assignment_4_solution -[ 38%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 -make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 37%] Built target demo_tutorial_a_first_example_solution_5 +[ 37%] Built target demo_unassigned_or_unused_file_readwrite make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/depend +[ 38%] Built target demo_tutorial_realignment_step2 +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/depend +[ 38%] Built target demo_howto_filter_similar_sequences +[ 38%] Built target demo_dox_graph_algorithms_kruskals_algorithm +[ 38%] Built target demo_tutorial_a_first_example_solution_3 +make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/depend +[ 38%] Built target demo_tutorial_genome_annotations_assignment_4_solution +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/depend +[ 38%] Built target demo_dox_index_begin_range_goDown_representative_repLength +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend +[ 38%] Built target demo_tutorial_a_first_example_solution_2 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/DependInfo.cmake --color= +[ 38%] Built target demo_unassigned_or_unused_index_qgram_counts +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/DependInfo.cmake --color= [ 39%] Built target demo_tutorial_parsing_command_line_arguments_example_with_own_function +make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend +make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend +[ 39%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local_assignment1 +make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_2.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend +[ 39%] Built target demo_tutorial_a_first_example_solution_1 +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build -make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_code_encapsulation.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build +make -f demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build.make demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build +make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_get_terminal_size.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build -[ 39%] Built target demo_tutorial_a_first_example_solution_1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/depend -[ 39%] Built target demo_tutorial_a_first_example_solution_2 -[ 39%] Built target demo_tutorial_a_first_example_code_encapsulation -make -f demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build -[ 39%] Built target demo_dox_misc_get_terminal_size -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/depend -make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_basic_code.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 39%] Built target demo_tutorial_seed_and_extend_example3 -make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/depend -[ 39%] Built target demo_tutorial_a_first_example_basic_code -[ 39%] Built target demo_tutorial_consensus_alignment_with_positions -make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/DependInfo.cmake --color= -[ 40%] Built target demo_tutorial_seed_and_extend_solution4 -[ 40%] Built target demo_tutorial_vcf_io_example1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string2.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_store_store_example.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_custom_file_endings.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/depend -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build -[ 40%] Built target demo_tutorial_journaled_set_solution_online_search_assignment3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build make -f demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build.make demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_graph_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build +make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/build +make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/build +make -f demos/CMakeFiles/demo_dox_sequence_string2.dir/build.make demos/CMakeFiles/demo_dox_sequence_string2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_string2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_custom_file_endings.dir/build.make demos/CMakeFiles/demo_howto_custom_file_endings.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example7.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_efficiently_import_sequences.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_alphabet.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_store_store_example.dir/build.make demos/CMakeFiles/demo_dox_store_store_example.dir/build -make -f demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build.make demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_custom_file_endings.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_string2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basic_techniques_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_tutorial_sam_and_bam_io_example7 -make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_store_store_example.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_consensus_alignment_with_positions.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_custom_file_endings.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake --color= -[ 40%] Built target demo_tutorial_alignment_graph_assignment1 +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_store_store_example.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_solution2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 40%] Built target demo_howto_efficiently_import_sequences +[ 39%] Built target demo_tutorial_a_first_example_code_encapsulation +[ 39%] Built target demo_dox_misc_get_terminal_size +[ 39%] Built target demo_tutorial_seed_and_extend_example3 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/depend +[ 39%] Built target demo_tutorial_vcf_io_example1 +[ 39%] Built target demo_tutorial_a_first_example_basic_code make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/depend +[ 40%] Built target demo_tutorial_seed_and_extend_solution4 +[ 40%] Built target demo_tutorial_alignment_graph_assignment1 make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/depend -[ 40%] Built target demo_dox_sequence_string2 -[ 41%] Built target demo_howto_custom_file_endings -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 41%] Built target demo_unassigned_or_unused_alphabet -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/depend +[ 40%] Built target demo_tutorial_journaled_set_solution_online_search_assignment3 +[ 40%] Built target demo_tutorial_sam_and_bam_io_example7 make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/depend -[ 41%] Built target demo_tutorial_basic_techniques_base +[ 40%] Built target demo_unassigned_or_unused_alphabet +[ 40%] Built target demo_tutorial_consensus_alignment_with_positions make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/DependInfo.cmake --color= +[ 40%] Built target demo_howto_efficiently_import_sequences +[ 41%] Built target demo_howto_custom_file_endings +make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend +[ 41%] Built target demo_dox_sequence_string2 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 41%] Built target demo_tutorial_basic_techniques_base cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_segment.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend [ 41%] Built target demo_dox_store_store_example make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/depend +make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/depend +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/DependInfo.cmake --color= -[ 41%] Built target demo_tutorial_bed_io_solution2 -make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/depend +make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/depend +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake --color= +[ 41%] Built target demo_tutorial_bed_io_solution2 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend [ 41%] Built target demo_tutorial_sam_and_bam_io_example2 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_sequence_segment.dir/build.make demos/CMakeFiles/demo_dox_sequence_segment.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_segment.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build.make demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_segment.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_transitive_closure.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_container_view_zip.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_depth_first_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build -[ 41%] Built target demo_dox_sequence_segment -make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/depend -[ 41%] Built target demo_dox_graph_algorithms_transitive_closure make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build -[ 43%] Built target demo_dox_graph_algorithms_depth_first_search -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build'. +make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/build +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/depend -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/depend -[ 43%] Built target demo_dox_sequence_container_view_zip +make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_seed_and_extend_example1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_realignment_step1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_suffix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/depend -[ 43%] Built target demo_dox_sequence_UNUSED_suffix -[ 43%] Built target demo_tutorial_indexed_fasta_io_base -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build -make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_counting.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_msa.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_length_countSequences.dir/DependInfo.cmake --color= -[ 43%] Built target demo_unassigned_or_unused_segmentalignment -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/DependInfo.cmake --color= -[ 43%] Built target demo_dox_align_split_split_alignment -make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build -[ 43%] Built target demo_tutorial_multiple_sequence_alignment_msa +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_split_split_alignment.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build.make demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_modified_string_nested.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_counting.dir/build.make demos/CMakeFiles/demo_dox_index_counting.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_counting.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_realignment_step1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build.make demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_counting.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_segmentalignment.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_cyclic_shape.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_length_countSequences.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_modifier_modified_string_nested make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build.make demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build -make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_interval_tree_example.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_realignment_step1 +[ 41%] Built target demo_dox_graph_algorithms_transitive_closure +[ 41%] Built target demo_dox_sequence_segment +[ 41%] Built target demo_dox_sequence_container_view_zip +[ 41%] Built target demo_tutorial_indexed_fasta_io_base +[ 43%] Built target demo_dox_graph_algorithms_depth_first_search +[ 43%] Built target demo_tutorial_seed_and_extend_example1 +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/depend +[ 43%] Built target demo_dox_sequence_UNUSED_suffix +make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/depend +make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/depend make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build -[ 43%] Built target demo_dox_index_counting +[ 43%] Built target demo_dox_align_split_split_alignment +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/DependInfo.cmake --color= +[ 43%] Built target demo_unassigned_or_unused_segmentalignment make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/depend +[ 43%] Built target demo_tutorial_multiple_sequence_alignment_msa +[ 43%] Built target demo_dox_modifier_modified_string_nested +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/DependInfo.cmake --color= +[ 43%] Built target demo_dox_index_counting +make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend +make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/DependInfo.cmake --color= -[ 43%] Built target demo_dox_modifier_cyclic_shape -[ 43%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/depend -make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/depend -[ 43%] Built target demo_tutorial_journaled_set_example_online_search -[ 43%] Built target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters +make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/depend +make -f demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/DependInfo.cmake --color= -[ 43%] Built target demo_dox_index_length_countSequences -make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/depend -make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/depend +[ 43%] Built target demo_tutorial_journaled_set_example_online_search +[ 43%] Built target demo_tutorial_realignment_step1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_queue_example.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/DependInfo.cmake --color= -[ 43%] Built target demo_dox_misc_interval_tree_example make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/depend -[ 43%] Built target demo_tutorial_background_and_motivation_example +[ 43%] Built target demo_dox_modifier_cyclic_shape +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/depend +make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/depend +[ 43%] Built target demo_dox_index_length_countSequences make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_graph.dir/DependInfo.cmake --color= +[ 43%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_specialised make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_sufarray.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/depend +[ 43%] Built target demo_dox_misc_interval_tree_example make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seeds_example1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_open_save.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build make -f demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_sequence_count_generic_characters.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build +make -f demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build.make demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_blast_io_write_assignment.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_background_and_motivation_example.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build make -f demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build.make demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build make -f demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build.make demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/build make -f demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_sufarray.dir/build.make demos/CMakeFiles/demo_dox_index_sufarray.dir/build +make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/build +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_parallel_queue_example.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_textAt_indexText_saAt_indexRequire.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build -[ 43%] Built target demo_tutorial_blast_io_write_assignment make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_metaprogramming_control.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_dox_parallel_queue_example +make -f demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build.make demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build +[ 43%] Built target demo_unassigned_or_unused_tutorial_sequence_count_generic_characters make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_sufarray.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_affine_dgs.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_graph.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 43%] Built target demo_tutorial_alignment_scoring_scheme_affine_dgs -make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/depend -[ 43%] Built target demo_tutorial_indexed_fasta_io_solution2 -[ 43%] Built target demo_dox_index_textAt_indexText_saAt_indexRequire -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/depend -make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/depend -[ 43%] Built target demo_tutorial_indices_fm_index -[ 43%] Built target demo_dox_index_sufarray -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/depend -make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend -[ 44%] Built target demo_tutorial_alignment_graph -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_open_save.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_node_predicate.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake --color= -[ 44%] Built target demo_tutorial_seeds_example1 -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake --color= -[ 44%] Built target demo_dox_basic_metaprogramming_control -make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_sufarray.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_open_save.dir/build.make demos/CMakeFiles/demo_dox_index_open_save.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_fm_index.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_open_save.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_node_predicate.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build +make -f demos/CMakeFiles/demo_dox_index_node_predicate.dir/build.make demos/CMakeFiles/demo_dox_index_node_predicate.dir/build +make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/depend +make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seeds_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/build +[ 43%] Built target demo_tutorial_blast_io_write_assignment +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_open_save.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_node_predicate.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_mums.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Built target demo_tutorial_pattern_matching_assignment3_solution -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mums.dir/DependInfo.cmake --color= +[ 43%] Built target demo_tutorial_background_and_motivation_example +[ 43%] Built target demo_tutorial_indexed_fasta_io_solution2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 44%] Built target demo_dox_index_open_save -make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build -[ 45%] Built target demo_dox_index_node_predicate +[ 43%] Built target demo_dox_index_textAt_indexText_saAt_indexRequire +make -f demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build.make demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/depend +[ 43%] Built target demo_dox_parallel_queue_example +[ 43%] Built target demo_dox_basic_metaprogramming_control +[ 43%] Built target demo_tutorial_alignment_scoring_scheme_affine_dgs +make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/depend +[ 43%] Built target demo_dox_index_sufarray +[ 43%] Built target demo_tutorial_indices_fm_index +[ 44%] Built target demo_tutorial_alignment_graph make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/depend -[ 45%] Built target demo_tutorial_sequences_base make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/depend -[ 46%] Built target demo_dox_modifier_modified_string -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build'. -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 44%] Built target demo_dox_index_open_save +[ 44%] Built target demo_tutorial_pattern_matching_assignment3_solution make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/depend -[ 46%] Built target demo_tutorial_q_gram_index_index_qgram -[ 46%] Built target demo_dox_index_mums make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/depend make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/depend make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_q_gram_index_index_qgram.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake --color= +[ 44%] Built target demo_tutorial_seeds_example1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake --color= -[ 46%] Built target demo_tutorial_sequences_assignment_4_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_maxrepeats.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/DependInfo.cmake --color= -[ 46%] Built target demo_tutorial_simple_rna_seq_base -[ 46%] Built target demo_tutorial_alignment_align_assignment1 +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_base.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_base.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/depend -make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_modified_string.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 45%] Built target demo_dox_index_node_predicate cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build +make -f demos/CMakeFiles/demo_dox_index_mums.dir/build.make demos/CMakeFiles/demo_dox_index_mums.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_4_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_mums.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build +[ 45%] Built target demo_tutorial_q_gram_index_index_qgram +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build.make demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build -make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build +make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_modified_string_mod_view.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_infix.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_align_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build +make -f demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake --color= +[ 46%] Built target demo_dox_modifier_modified_string +make -f demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build.make demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/depend +[ 46%] Built target demo_tutorial_sequences_base make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_solution4.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_modifier_modified_string_mod_view +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_maxrepeats.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build.make demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build make -f demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build.make demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 46%] Built target demo_tutorial_sequences_assignment_4_solution make -f demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build.make demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build +[ 46%] Built target demo_dox_index_mums +make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_blast_blast_in_lowlevel.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 46%] Built target demo_dox_sequence_UNUSED_infix -[ 46%] Built target demo_tutorial_seed_and_extend_solution3 -[ 46%] Built target demo_tutorial_parsing_command_line_arguments_base -[ 46%] Built target demo_dox_index_maxrepeats -make -f demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build.make demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_bed_io_UNUSED_bed_stream_read.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build -make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/depend +[ 46%] Built target demo_dox_modifier_modified_string_mod_view +[ 46%] Built target demo_tutorial_simple_rna_seq_base make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_load_score.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_consensus_consensus_alignment.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution4 +make -f demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build.make demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build +[ 46%] Built target demo_tutorial_alignment_align_assignment1 make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/DependInfo.cmake --color= -[ 47%] Built target demo_dox_consensus_consensus_alignment +[ 46%] Built target demo_tutorial_parsing_command_line_arguments_base +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend +[ 46%] Built target demo_dox_sequence_UNUSED_infix +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake --color= -[ 47%] Built target demo_blast_blast_in_lowlevel -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/DependInfo.cmake --color= -[ 47%] Built target demo_dox_bed_io_UNUSED_bed_stream_read -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/depend make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend +[ 47%] Built target demo_unassigned_or_unused_tutorials_custim_io_solution4 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_supermaxrepeats.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/DependInfo.cmake --color= -[ 47%] Built target demo_dox_index_supermaxrepeats +make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_scores_load_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_scores_load_score.dir/build.make demos/CMakeFiles/demo_howto_scores_load_score.dir/build -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/DependInfo.cmake --color= +[ 47%] Built target demo_tutorial_seed_and_extend_solution3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_scores_load_score.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake --color= +[ 47%] Built target demo_dox_index_maxrepeats +make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_blast_blast_in_lowlevel +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build.make demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build +[ 47%] Built target demo_dox_bed_io_UNUSED_bed_stream_read +[ 47%] Built target demo_dox_consensus_consensus_alignment +make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_zip_iterator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend +[ 47%] Built target demo_dox_index_supermaxrepeats +make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_bellman_ford_algorithm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_metaprogramming_logic.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake --color= +[ 47%] Built target demo_howto_scores_load_score +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build -[ 47%] Built target demo_howto_scores_load_score +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build -[ 47%] Built target demo_dox_basic_zip_iterator -make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_scoring_scheme_matrix.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_2_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_dox_basic_zip_iterator make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build +make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 47%] Built target demo_dox_graph_algorithms_bellman_ford_algorithm -[ 47%] Built target demo_tutorial_bed_io_base -make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/DependInfo.cmake --color= -[ 47%] Built target demo_tutorial_seed_and_extend_solution5 -[ 47%] Built target demo_dox_basic_metaprogramming_logic -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/DependInfo.cmake --color= -[ 47%] Built target demo_tutorial_alignment_scoring_scheme_matrix -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/depend -[ 48%] Built target demo_tutorial_sam_and_bam_io_solution2 -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend -[ 49%] Built target demo_tutorial_iterators_assignment_2_solution -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/DependInfo.cmake --color= -[ 49%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 +make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build.make demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build +make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_generic_programming_example_hashing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_align_graph_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_dox_graph_algorithms_bellman_ford_algorithm +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/depend +make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_enable_if.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build.make demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build +make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build.make demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_stringset.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_example_tempSubclassing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_parallel_splitter_example.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_getOccurrences_getFrequency_range_getFibre.dir/build'. +[ 47%] Built target demo_dox_basic_metaprogramming_logic make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 49%] Built target demo_tutorial_generic_programming_example_hashing -make -f demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build -make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build -[ 50%] Built target demo_dox_graph_align_graph_align make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_enable_if.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 47%] Built target demo_tutorial_bed_io_base +[ 47%] Built target demo_tutorial_alignment_scoring_scheme_matrix +[ 48%] Built target demo_tutorial_iterators_assignment_2_solution +[ 49%] Built target demo_tutorial_sam_and_bam_io_solution2 make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/depend -[ 50%] Built target demo_dox_parallel_splitter_example -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 49%] Built target demo_tutorial_seed_and_extend_solution5 make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/DependInfo.cmake --color= -[ 50%] Built target demo_tutorial_a_first_example_example_tempSubclassing -[ 50%] Built target demo_dox_index_getOccurrences_getFrequency_range_getFibre +[ 49%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step1 make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/build make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake --color= -[ 50%] Built target demo_dox_index_begin_atEnd_representative make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/depend +[ 49%] Built target demo_tutorial_a_first_example_example_tempSubclassing +[ 50%] Built target demo_dox_graph_align_graph_align +[ 50%] Built target demo_tutorial_generic_programming_example_hashing +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_stringset.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_begin_atEnd_representative.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake --color= -[ 50%] Built target demo_tutorial_bed_io_example1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake --color= -[ 50%] Built target demo_dox_basic_enable_if -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/depend -[ 51%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_parallel_splitter_example +make -f demos/CMakeFiles/demo_dox_basic_enable_if.dir/build.make demos/CMakeFiles/demo_dox_basic_enable_if.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_enable_if.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_index_getOccurrences_getFrequency_range_getFibre make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build +make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_stringset.dir/build.make demos/CMakeFiles/demo_dox_sequence_stringset.dir/build +[ 50%] Built target demo_tutorial_bed_io_example1 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_blastn.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 50%] Built target demo_dox_index_begin_atEnd_representative +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build -[ 52%] Built target demo_dox_sequence_stringset -make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/depend +make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_stringset.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_global_alignment_unbanded.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_metaprogramming_math.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build'. +make -f demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build.make demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build +[ 50%] Built target demo_dox_basic_enable_if +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_begin_atEnd_representative_bottomUp.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_benchmark_stream.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build +make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build +[ 51%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_blastn +[ 52%] Built target demo_dox_sequence_stringset +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_index.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/depend [ 52%] Built target demo_dox_align_global_alignment_unbanded make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_2_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 52%] Built target demo_dox_basic_metaprogramming_math -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 52%] Built target demo_unassigned_or_unused_benchmark_stream -make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/depend -make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/depend -[ 53%] Built target demo_dox_index_begin_atEnd_representative_bottomUp -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/DependInfo.cmake --color= -[ 53%] Built target demo_tutorial_pattern_matching_find_index make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_all_pairs_shortest_path.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_local.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build +make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_finder.dir/DependInfo.cmake --color= -[ 53%] Built target demo_tutorial_a_first_example_base -[ 53%] Built target demo_tutorial_sequences_assignment_2_solution -[ 54%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/depend make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_online.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend -[ 55%] Built target demo_tutorial_fragment_store_access_aligned_reads2 -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/DependInfo.cmake --color= -[ 55%] Built target demo_dox_graph_algorithms_all_pairs_shortest_path -make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_longest_common_subsequence.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_finder.dir/build.make demos/CMakeFiles/demo_dox_index_finder.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build +[ 52%] Built target demo_dox_basic_metaprogramming_math +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/depend +[ 52%] Built target demo_dox_graph_algorithms_all_pairs_shortest_path +[ 53%] Built target demo_dox_index_begin_atEnd_representative_bottomUp make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_bam_io_bam_tags_dict.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_gaps_example.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_file_speed.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/depend +[ 53%] Built target demo_unassigned_or_unused_benchmark_stream make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_finder.dir/build'. +[ 53%] Built target demo_tutorial_pattern_matching_find_index make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_find_finder_online.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/build -[ 56%] Built target demo_dox_graph_algorithms_longest_common_subsequence -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build +[ 54%] Built target demo_tutorial_sequences_assignment_2_solution +[ 54%] Built target demo_tutorial_fragment_store_access_aligned_reads2 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 58%] Built target demo_dox_bam_io_bam_tags_dict -make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build -[ 58%] Built target demo_dox_index_finder +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/DependInfo.cmake --color= +[ 54%] Built target demo_tutorial_a_first_example_base +[ 55%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_local make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_gaps_example.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 59%] Built target demo_unassigned_or_unused_file_speed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/depend +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/depend -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_index_iterator_short.dir/build.make demos/CMakeFiles/demo_dox_index_iterator_short.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/DependInfo.cmake --color= -[ 60%] Built target demo_dox_find_finder_online -[ 60%] Built target demo_tutorial_simple_rna_seq_interval_tree -[ 60%] Built target demo_tutorial_parsing_command_line_arguments_final_solution make -f demos/CMakeFiles/demo_dox_sequence_string.dir/build.make demos/CMakeFiles/demo_dox_sequence_string.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator_short.dir/DependInfo.cmake --color= -[ 60%] Built target demo_dox_align_gaps_example make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_align_integrate_align.dir/build.make demos/CMakeFiles/demo_dox_align_integrate_align.dir/depend -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_find_finder_online.dir/build.make demos/CMakeFiles/demo_dox_find_finder_online.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_interval_tree.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 56%] Built target demo_dox_graph_algorithms_longest_common_subsequence make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_string.dir/DependInfo.cmake --color= -[ 60%] Built target demo_dox_graph_algorithms_strongly_connected_components -[ 60%] Built target demo_dox_index_UNUSED_shape +[ 58%] Built target demo_dox_bam_io_bam_tags_dict +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator_short.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/DependInfo.cmake --color= +[ 59%] Built target demo_unassigned_or_unused_file_speed +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_integrate_align.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_find_finder_online.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 59%] Built target demo_dox_index_finder +make -f demos/CMakeFiles/demo_dox_align_gaps_example.dir/build.make demos/CMakeFiles/demo_dox_align_gaps_example.dir/build +make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_gaps_example.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build +make -f demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build +[ 59%] Built target demo_tutorial_simple_rna_seq_interval_tree make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_final_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_example_tags.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_iterator_short.dir/build.make demos/CMakeFiles/demo_dox_index_iterator_short.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_types_graph_algo_dijkstra.dir/build'. +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_strongly_connected_components.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_sequence_string.dir/build.make demos/CMakeFiles/demo_dox_sequence_string.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_iterator_short.dir/build.make demos/CMakeFiles/demo_dox_index_iterator_short.dir/build +make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_iterator_short.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 60%] Built target demo_dox_find_finder_online make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_string.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_integrate_align.dir/build.make demos/CMakeFiles/demo_dox_align_integrate_align.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_integrate_align.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_iterator_short.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_graph_types_graph_algo_dijkstra +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build +make -f demos/CMakeFiles/demo_dox_align_integrate_align.dir/build.make demos/CMakeFiles/demo_dox_align_integrate_align.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build.make demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_display_aligned_reads.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build.make demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_4_templateSubclassing.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_integrate_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_tutorial_a_first_example_example_tags -[ 60%] Built target demo_tutorial_gff_and_gtf_io_solution3 -[ 60%] Built target demo_dox_index_iterator_short +[ 60%] Built target demo_dox_align_gaps_example +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_bam_io_bam_file_in.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/depend +make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_extend_extend_alignment.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 60%] Built target demo_dox_sequence_string -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/depend -[ 61%] Built target demo_dox_align_integrate_align -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/depend -make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend -make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/DependInfo.cmake --color= +[ 60%] Built target demo_tutorial_parsing_command_line_arguments_final_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake --color= -[ 61%] Built target demo_tutorial_fragment_store_display_aligned_reads -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake --color= -[ 61%] Built target demo_tutorial_a_first_example_solution_4_templateSubclassing +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/DependInfo.cmake --color= -[ 61%] Built target demo_dox_align_extend_extend_alignment +[ 60%] Built target demo_dox_graph_algorithms_strongly_connected_components +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/DependInfo.cmake --color= +[ 60%] Built target demo_tutorial_a_first_example_example_tags +[ 60%] Built target demo_dox_graph_types_graph_algo_dijkstra +[ 60%] Built target demo_dox_index_UNUSED_shape +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/depend +make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/depend make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/depend -[ 61%] Built target demo_dox_bam_io_bam_file_in make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake --color= +[ 60%] Built target demo_dox_sequence_string +[ 60%] Built target demo_tutorial_gff_and_gtf_io_solution3 make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/depend -make -f demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build.make demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build.make demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/DependInfo.cmake --color= +[ 60%] Built target demo_dox_index_iterator_short +[ 60%] Built target demo_tutorial_fragment_store_display_aligned_reads +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/depend +[ 60%] Built target demo_tutorial_a_first_example_solution_4_templateSubclassing +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_align.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/depend +[ 61%] Built target demo_dox_align_integrate_align +make -f demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build.make demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake --color= +[ 61%] Built target demo_dox_bam_io_bam_file_in +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build +[ 61%] Built target demo_dox_align_extend_extend_alignment +make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_blast_io_read_assignment.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake --color= +[ 61%] Built target demo_tutorial_blast_io_read_assignment +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build -make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build'. make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build.make demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build +make -f demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build.make demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_metaprogramming_switch.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tabix_io_tabix_vcf.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build.make demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 61%] Built target demo_tutorial_blast_io_read_assignment -[ 61%] Built target demo_tutorial_vcf_io_solution1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_property_maps.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_align.dir/build.make demos/CMakeFiles/demo_dox_align_align.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build -[ 62%] Built target demo_tabix_io_tabix_vcf -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/depend -make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/depend -[ 62%] Built target demo_tutorial_simple_rna_seq_genequant_solution1 -[ 62%] Built target demo_tutorial_index_iterators_index_property_maps -make -f demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/depend -make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/DependInfo.cmake --color= -[ 62%] Built target demo_dox_basic_metaprogramming_switch -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/DependInfo.cmake --color= -[ 62%] Built target demo_unassigned_or_unused_gff2gtf -[ 62%] Built target demo_dox_arg_parse_argument_parser -make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/depend -[ 62%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 -[ 63%] Built target demo_dox_align_align -make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/depend -make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/depend -make -f demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build.make demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_arg_parse_argument_parser.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build.make demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_align.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_gff_io_UNUSED_gff_stream_read.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_gff2gtf.dir/build'. make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_dag_shortest_path.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 61%] Built target demo_tutorial_simple_rna_seq_genequant_solution1 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build.make demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_dijkstra.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_floyd_warshall_algorithm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build -[ 63%] Built target demo_dox_graph_algorithms_dijkstra -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_dox_graph_algorithms_dag_shortest_path +[ 61%] Built target demo_dox_basic_metaprogramming_switch +make -f demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build +[ 61%] Built target demo_tutorial_vcf_io_solution1 +[ 61%] Built target demo_tutorial_index_iterators_index_property_maps +make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/depend +make -f demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build.make demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/depend +make -f demos/CMakeFiles/demo_howto_scores_init_score.dir/build.make demos/CMakeFiles/demo_howto_scores_init_score.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_segments.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_ford_fulkerson_algorithm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 63%] Built target demo_dox_gff_io_UNUSED_gff_stream_read -[ 63%] Built target demo_tutorial_parsing_command_line_arguments_example1 -make -f demos/CMakeFiles/demo_howto_scores_init_score.dir/build.make demos/CMakeFiles/demo_howto_scores_init_score.dir/depend -[ 64%] Built target demo_tutorial_a_first_example_solution_4 -make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/depend -make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/depend -make -f demos/CMakeFiles/demo_dox_index_mummy.dir/build.make demos/CMakeFiles/demo_dox_index_mummy.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_scores_init_score.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/DependInfo.cmake --color= -[ 64%] Built target demo_dox_misc_name_store_cache -[ 64%] Built target demo_dox_graph_algorithms_floyd_warshall_algorithm +[ 62%] Built target demo_tabix_io_tabix_vcf +[ 62%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step5 +make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/depend +[ 62%] Built target demo_unassigned_or_unused_gff2gtf +[ 62%] Built target demo_dox_arg_parse_argument_parser +make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/depend +[ 62%] Built target demo_tutorial_parsing_command_line_arguments_example1 +[ 63%] Built target demo_dox_align_align +make -f demos/CMakeFiles/demo_dox_index_mummy.dir/build.make demos/CMakeFiles/demo_dox_index_mummy.dir/depend +[ 64%] Built target demo_tutorial_a_first_example_solution_4 make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/depend -[ 64%] Built target demo_tutorial_sequences_example_segments -[ 64%] Built target demo_dox_graph_algorithms_ford_fulkerson_algorithm -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/depend make -f demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/DependInfo.cmake --color= +[ 64%] Built target demo_dox_gff_io_UNUSED_gff_stream_read make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/depend -[ 64%] Built target demo_dox_stream_lexical_cast make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/DependInfo.cmake --color= +[ 64%] Built target demo_dox_graph_algorithms_dag_shortest_path +[ 64%] Built target demo_dox_graph_algorithms_dijkstra +[ 64%] Built target demo_dox_graph_algorithms_floyd_warshall_algorithm make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_mummy.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/DependInfo.cmake --color= +[ 64%] Built target demo_tutorial_sequences_example_segments +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build.make demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build +make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build.make demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_dox_graph_algorithms_ford_fulkerson_algorithm +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_name_store_cache.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_stream_lexical_cast.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_howto_scores_init_score.dir/build.make demos/CMakeFiles/demo_howto_scores_init_score.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_howto_scores_init_score.dir/build.make demos/CMakeFiles/demo_howto_scores_init_score.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build +make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_scores_init_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build +make -f demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_index_mummy.dir/build.make demos/CMakeFiles/demo_dox_index_mummy.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats make -f demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_heaviest_increasing_subsequence.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_mummy.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build +[ 64%] Built target demo_dox_misc_name_store_cache make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment6_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_longest_increasing_subsequence.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_breadth_first_search.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_solution_6.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_dox_graph_algorithms_heaviest_increasing_subsequence -[ 64%] Built target demo_howto_scores_init_score -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/depend -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/depend -make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/depend -[ 64%] Built target demo_dox_align_profile_profile_seq_score -[ 64%] Built target demo_tutorial_a_first_example_solution_6 -[ 64%] Built target demo_dox_graph_algorithms_longest_increasing_subsequence -[ 64%] Built target demo_dox_index_mummy -make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/depend -make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/depend -make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/DependInfo.cmake --color= -[ 64%] Built target demo_tutorial_sequences_example_conversions_copy -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend -[ 64%] Built target demo_tutorial_parsing_command_line_arguments_assignment6_solution -[ 64%] Built target demo_dox_graph_algorithms_breadth_first_search -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend -make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake --color= +[ 64%] Built target demo_dox_stream_lexical_cast make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_conversions_copy.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_mummy.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_unassigned_or_unused_tutorial_file_io_stream_compression_formats +[ 64%] Built target demo_howto_scores_init_score make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build +make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_profile_profile_seq_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 64%] Built target demo_dox_graph_algorithms_breadth_first_search make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build -make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_chaining.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/build +make -f demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build +make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/depend +make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_find_repeats.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_find_repeats.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build +[ 64%] Built target demo_dox_index_mummy +[ 64%] Built target demo_tutorial_a_first_example_solution_6 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_iterator.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_extension.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 64%] Built target demo_tutorial_bed_io_solution3 -[ 65%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 +[ 64%] Built target demo_dox_graph_algorithms_heaviest_increasing_subsequence +[ 64%] Built target demo_tutorial_parsing_command_line_arguments_assignment6_solution +make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/depend +[ 64%] Built target demo_dox_graph_algorithms_longest_increasing_subsequence make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/depend +[ 64%] Built target demo_tutorial_sequences_example_conversions_copy +[ 64%] Built target demo_tutorial_bed_io_solution3 make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/depend -[ 65%] Built target demo_dox_seeds_seeds_chaining make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/depend -[ 65%] Built target demo_dox_seeds_seeds_extension -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake --color= +[ 65%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step4 make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/depend -[ 65%] Built target demo_dox_graph_algorithms_prims_algorithm -[ 65%] Built target demo_tutorial_graph_graph_hmm make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/depend -[ 65%] Built target demo_dox_index_find_repeats make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake --color= -[ 65%] Built target demo_tutorial_simple_rna_seq_genequant_solution3 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake --color= -[ 66%] Built target demo_dox_index_iterator -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_prims_algorithm.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_iterator.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/depend -make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend +[ 65%] Built target demo_dox_seeds_seeds_chaining +[ 65%] Built target demo_dox_align_profile_profile_seq_score make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/DependInfo.cmake --color= -[ 66%] Built target demo_dox_seeds_seeds_add_seed make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build +make -f demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_index_find_repeats.dir/build.make demos/CMakeFiles/demo_dox_index_find_repeats.dir/build +[ 65%] Built target demo_dox_seeds_seeds_extension +[ 65%] Built target demo_dox_graph_algorithms_prims_algorithm +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build.make demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_graph_hmm.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_find_repeats.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_iterator.dir/build.make demos/CMakeFiles/demo_dox_index_iterator.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_size.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seeds_seeds_add_seed.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_assignment_2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build +make -f demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build.make demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_final_result.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_iterator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_UNUSED_shape_hash_next.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_assignment_1_solution.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_iterator.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build -[ 66%] Built target demo_tutorial_alphabets_example_size -[ 66%] Built target demo_tutorial_a_first_example_final_result make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 66%] Built target demo_dox_index_UNUSED_shape_hash_next -make -f demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build -[ 67%] Built target demo_tutorial_string_sets_assignment_2 -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/depend -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_tutorial_graph_graph_hmm +make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build +[ 65%] Built target demo_dox_index_find_repeats +[ 65%] Built target demo_tutorial_simple_rna_seq_genequant_solution3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_nested.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 65%] Built target demo_dox_seeds_seeds_add_seed make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/depend -[ 67%] Built target demo_unassigned_or_unused_iterator -[ 67%] Built target demo_tutorial_pattern_matching_assignment2 +[ 65%] Built target demo_tutorial_alphabets_example_size make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/DependInfo.cmake --color= -[ 68%] Built target demo_tutorial_alphabets_assignment_1_solution make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/depend make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/depend make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/depend +[ 66%] Built target demo_tutorial_a_first_example_final_result +[ 66%] Built target demo_tutorial_string_sets_assignment_2 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/depend +[ 67%] Built target demo_dox_index_iterator make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/DependInfo.cmake --color= -[ 69%] Built target demo_tutorial_simple_rna_seq_genequant_assignment1 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/DependInfo.cmake --color= +[ 68%] Built target demo_tutorial_alphabets_assignment_1_solution +[ 68%] Built target demo_tutorial_pattern_matching_assignment2 +[ 68%] Built target demo_dox_index_UNUSED_shape_hash_next +make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/depend +make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/depend -[ 69%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_allocator.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build -[ 69%] Built target demo_tutorial_modifiers_nested make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_score_score.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_parse_lm_stellar.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake --color= +[ 68%] Built target demo_unassigned_or_unused_iterator +[ 68%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step2 +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_bitsPerValue.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake --color= +[ 68%] Built target demo_tutorial_modifiers_nested make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend +[ 68%] Built target demo_tutorial_alphabets_example_bitsPerValue +[ 69%] Built target demo_tutorial_simple_rna_seq_genequant_assignment1 +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_base.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build +[ 70%] Built target demo_unassigned_or_unused_parse_lm_stellar +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build.make demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alphabets_example_ordValue.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build.make demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build -[ 70%] Built target demo_unassigned_or_unused_parse_lm_stellar +make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/build +make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment2_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 70%] Built target demo_tutorial_alphabets_example_bitsPerValue -make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_allocator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_score_score.dir/build.make demos/CMakeFiles/demo_dox_score_score.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build -[ 70%] Built target demo_tutorial_sam_and_bam_io_base -[ 70%] Built target demo_tutorial_alphabets_example_ordValue make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/build -[ 70%] Built target demo_tutorial_index_iterators_iterator_solution1 +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_score_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 72%] Built target demo_tutorial_pattern_matching_assignment2_solution -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/depend -[ 73%] Built target demo_tutorial_basics_allocator -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/depend -make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_base.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/DependInfo.cmake --color= -[ 74%] Built target demo_dox_score_score +make -f demos/CMakeFiles/demo_tutorial_basics_base.dir/build.make demos/CMakeFiles/demo_tutorial_basics_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build.make demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build -[ 74%] Built target demo_tutorial_basics_base -[ 74%] Built target demo_tutorial_pattern_matching_assignment1_solution -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/depend +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_show_alphabets.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 70%] Built target demo_tutorial_sam_and_bam_io_base make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_parse_gff2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_bed_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_bidirectional_search.dir/build'. +[ 70%] Built target demo_tutorial_alphabets_example_ordValue +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build +[ 72%] Built target demo_tutorial_pattern_matching_assignment2_solution make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build make -f demos/CMakeFiles/demo_tutorial_iterators_base.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_base.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_base.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 73%] Built target demo_tutorial_basics_allocator +[ 74%] Built target demo_dox_score_score +make -f demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build.make demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build [ 74%] Built target demo_tutorial_basics_show_alphabets -[ 74%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/depend make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build -[ 75%] Built target demo_tutorial_index_iterators_index_bidirectional_search +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/DependInfo.cmake --color= -[ 75%] Built target demo_tutorial_bed_io_solution1 -[ 75%] Built target demo_tutorial_pattern_matching_assignment1 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/depend -[ 75%] Built target demo_tutorial_iterators_base -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake --color= +[ 74%] Built target demo_tutorial_pattern_matching_assignment1_solution +[ 74%] Built target demo_tutorial_index_iterators_iterator_solution1 make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_consensus_alignment_without_positions.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/DependInfo.cmake --color= -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_consensus_alignment_without_positions +[ 74%] Built target demo_tutorial_basics_base make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/depend +[ 74%] Built target demo_unassigned_or_unused_tutorials_custim_io_parse_gff2 +make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend +make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_alignment_align.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_file_io_overview_solution1 -make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/depend +[ 75%] Built target demo_tutorial_bed_io_solution1 +[ 75%] Built target demo_tutorial_index_iterators_index_bidirectional_search +make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake --color= +[ 75%] Built target demo_tutorial_pattern_matching_assignment1 +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 75%] Built target demo_tutorial_iterators_base make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build make -f demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build.make demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build -make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_standard.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/DependInfo.cmake --color= +[ 76%] Built target demo_tutorial_consensus_alignment_without_positions +[ 76%] Built target demo_tutorial_file_io_overview_solution1 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_modifier_cyclic_shape_snippets.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_alignment_align.dir/build.make demos/CMakeFiles/demo_tutorial_alignment_align.dir/build -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build +make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_align.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build -[ 76%] Built target demo_dox_modifier_cyclic_shape_snippets -[ 76%] Built target demo_tutorial_sam_and_bam_io_example1 -make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/depend -[ 76%] Built target demo_tutorial_file_io_overview_solution2 +make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_access_aligned_reads.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_alignment_align.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build +[ 76%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_standard make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_file_io_overview_solution3 -[ 76%] Built target demo_tutorial_alignment_align +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_hint.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build.make demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/depend -[ 76%] Built target demo_tutorial_genome_annotations_assignment_1_hint -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_solution4 -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_fragment_store_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_fragment_store_access_aligned_reads -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/depend +[ 76%] Built target demo_tutorial_file_io_overview_solution2 +[ 76%] Built target demo_dox_modifier_cyclic_shape_snippets make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/depend make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build.make demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_generic_programming_template_subclassing.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_statistics_load_markov_model.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build'. cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/DependInfo.cmake --color= -[ 76%] Built target demo_dox_statistics_load_markov_model -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_fragment_store_base -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build +[ 76%] Built target demo_tutorial_sam_and_bam_io_example1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment4_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/DependInfo.cmake --color= +[ 76%] Built target demo_tutorial_file_io_overview_solution3 [ 76%] Built target demo_tutorial_generic_programming_template_subclassing -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_fragment_store_access_aligned_reads make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/build -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/depend make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_genome_annotations_assignment_1_hint +[ 76%] Built target demo_tutorial_alignment_align +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/depend +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend +[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_solution4 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_2_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_iterators_assignment_3_workshop +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend +make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake --color= +[ 76%] Built target demo_tutorial_iterators_assignment_3_workshop make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_parsing_command_line_arguments_assignment4_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/DependInfo.cmake --color= +[ 76%] Built target demo_tutorial_fragment_store_base make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_modifiers_assignment1_solution -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build -[ 76%] Built target demo_tutorial_sequence_io_solution4 +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/depend -[ 76%] Built target demo_unassigned_or_unused_index_node_predicate +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/depend -[ 76%] Built target demo_tutorial_genome_annotations_assignment_2_solution make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/depend -[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_assignment3 +[ 76%] Built target demo_dox_statistics_load_markov_model make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build +make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/depend +[ 76%] Built target demo_tutorial_parsing_command_line_arguments_assignment4_solution +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake --color= -[ 76%] Built target demo_tutorial_parsing_command_line_arguments_assignment2_solution +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_assignment1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build +make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build +[ 76%] Built target demo_tutorial_sequence_io_solution4 make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_using_zip_iterator.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build +[ 76%] Built target demo_tutorial_genome_annotations_assignment_2_solution +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_index_node_predicate.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_assignment3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment2_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build.make demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_3_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_genome_annotations_assignment_3_solution +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build.make demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_base.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_modifiers_assignment1_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_solution_1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/depend +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_example2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_genome_annotations_base make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 76%] Built target demo_tutorial_gff_and_gtf_io_base +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_file_io_overview_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build.make demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_using_zip_iterator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/DependInfo.cmake --color= -[ 77%] Built target demo_tutorial_gff_and_gtf_io_example1 make -f demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/depend -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/depend +[ 76%] Built target demo_unassigned_or_unused_index_node_predicate +[ 76%] Built target demo_tutorial_simple_rna_seq_genequant_assignment3 +[ 76%] Built target demo_tutorial_gff_and_gtf_io_base +[ 76%] Built target demo_tutorial_parsing_command_line_arguments_assignment2_solution +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build -[ 77%] Built target demo_tutorial_gff_and_gtf_io_example2 -[ 77%] Built target demo_tutorial_file_io_overview_example1 -[ 77%] Built target demo_tutorial_gff_and_gtf_io_solution1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/DependInfo.cmake --color= -[ 77%] Built target demo_tutorial_graph_solution_1 -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/depend +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/depend make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/depend make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 76%] Built target demo_tutorial_genome_annotations_base +[ 76%] Built target demo_tutorial_genome_annotations_assignment_3_solution +[ 76%] Built target demo_tutorial_graph_solution_1 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_search.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build +make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_gff_and_gtf_io_solution2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_howto_using_zip_iterator +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/depend +[ 77%] Built target demo_tutorial_gff_and_gtf_io_example1 +make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend +[ 77%] Built target demo_tutorial_file_io_overview_example1 +[ 77%] Built target demo_tutorial_gff_and_gtf_io_example2 +make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend +[ 77%] Built target demo_tutorial_gff_and_gtf_io_solution1 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake --color= +[ 77%] Built target demo_howto_using_zip_iterator +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake --color= +[ 77%] Built target demo_tutorial_gff_and_gtf_io_solution2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build +[ 77%] Built target demo_tutorial_index_iterators_index_search +[ 77%] Built target demo_unassigned_or_unused_tutorial_file_io_mmap_string_example +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build +make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_graph_dijkstra.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_index_iterators_index_search -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_mmap_string_example.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 77%] Built target demo_tutorial_gff_and_gtf_io_solution2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment2.dir/build'. -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Built target demo_tutorial_graph_graph_dijkstra +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build make -f demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build.make demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_index.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build -[ 78%] Built target demo_unassigned_or_unused_tutorial_file_io_mmap_string_example -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build -make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/build +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_preorder.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/depend -[ 78%] Built target demo_tutorial_index_iterators_index_assignment2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build.make demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build -make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/DependInfo.cmake --color= -[ 78%] Built target demo_tutorial_index_iterators_index_assignment1 -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_simple_rna_seq_genequant_solution5.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build +make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_index_shape_hash_init.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 78%] Built target demo_tutorial_index_iterators_iterator_solution3 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_find_finder_index.dir/build.make demos/CMakeFiles/demo_dox_find_finder_index.dir/build -[ 78%] Built target demo_tutorial_simple_rna_seq_genequant_solution5 -make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_index_search2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/depend -[ 79%] Built target demo_tutorial_index_iterators_index_preorder -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_find_finder_index.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/DependInfo.cmake --color= -[ 79%] Built target demo_dox_index_shape_hash_init -[ 79%] Built target demo_tutorial_index_iterators_index_search2 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build.make demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build.make demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend -[ 79%] Built target demo_dox_find_finder_index -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build.make demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_find2_index_approx.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build'. +[ 78%] Built target demo_tutorial_graph_graph_dijkstra +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend +[ 78%] Built target demo_tutorial_index_iterators_index_assignment2 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build +[ 78%] Built target demo_tutorial_index_iterators_iterator_solution3 +[ 78%] Built target demo_tutorial_index_iterators_index_assignment1 make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_compute_alignment_stats.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_profile_profile_seq_frac_score.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build.make demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_vcf_io_base.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/depend +make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build +[ 79%] Built target demo_tutorial_index_iterators_index_preorder +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/depend +[ 79%] Built target demo_dox_find_finder_index +[ 79%] Built target demo_tutorial_simple_rna_seq_genequant_solution5 +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_assignment2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_indices_find2_index_approx -make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build -[ 79%] Built target demo_dox_align_profile_profile_seq_frac_score -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build.make demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/DependInfo.cmake --color= +[ 79%] Built target demo_dox_index_shape_hash_init make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 79%] Built target demo_tutorial_index_iterators_iterator_assignment2 -[ 79%] Built target demo_dox_align_compute_alignment_stats +[ 79%] Built target demo_tutorial_index_iterators_index_search2 make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/depend -[ 79%] Built target demo_tutorial_vcf_io_base make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend +[ 79%] Built target demo_dox_align_compute_alignment_stats make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build.make demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build +[ 79%] Built target demo_tutorial_indices_find2_index_approx +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_statistics_build_markov_model.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_index_iterators_iterator_solution2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake --color= +[ 79%] Built target demo_dox_align_profile_profile_seq_frac_score +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend +[ 79%] Built target demo_tutorial_vcf_io_base +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend +[ 79%] Built target demo_tutorial_index_iterators_iterator_assignment2 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_base.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend +make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build +[ 79%] Built target demo_dox_statistics_build_markov_model +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 80%] Built target demo_tutorial_index_iterators_iterator_solution2 -make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build -[ 80%] Built target demo_dox_statistics_build_markov_model make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indexed_fasta_io_solution1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_assignment_3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build +make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Built target demo_tutorial_index_iterators_iterator_solution2 make -f demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build.make demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build -[ 80%] Built target demo_tutorial_indexed_fasta_io_solution1 -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/depend -[ 80%] Built target demo_tutorial_sequences_assignment_3 -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/build +make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_genome_annotations_assignment_1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build -make -f demos/CMakeFiles/demo_tutorial_indices_base.dir/build.make demos/CMakeFiles/demo_tutorial_indices_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_assignment_1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build.make demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build -[ 81%] Built target demo_tutorial_genome_annotations_assignment_1_solution -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_example_tags_for_print.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_misc_enumerate_strings.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_align_global_alignment_banded.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 81%] Built target demo_dox_align_global_alignment_banded -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/depend -[ 81%] Built target demo_tutorial_indices_assignment_1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_base.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/DependInfo.cmake --color= -[ 82%] Built target demo_tutorial_a_first_example_example_tags_for_print +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorials_custim_io_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 82%] Built target demo_unassigned_or_unused_tutorials_custim_io_example1 -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/depend -[ 83%] Built target demo_dox_misc_enumerate_strings -make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Built target demo_tutorial_indices_base -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build -make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build +make -f demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build.make demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_3_workshop_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 83%] Built target demo_tutorial_iterators_assignment_1_solution -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build +make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build make -f demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build.make demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 80%] Built target demo_tutorial_indexed_fasta_io_solution1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build -[ 83%] Built target demo_tutorial_sequence_io_solution1 -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 84%] Built target demo_tutorial_indices_assignment_2 -make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/depend +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_indices_assignment_2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_4_workshop_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build +[ 81%] Built target demo_tutorial_genome_annotations_assignment_1_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend -[ 84%] Built target demo_tutorial_iterators_assignment_3_workshop_solution +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/DependInfo.cmake --color= +[ 81%] Built target demo_tutorial_sequences_assignment_3 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build +make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_howto_align_gaps_clipping.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 81%] Built target demo_tutorial_indices_assignment_1 +make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/depend +[ 81%] Built target demo_dox_align_global_alignment_banded +[ 82%] Built target demo_tutorial_a_first_example_example_tags_for_print make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/DependInfo.cmake --color= +[ 82%] Built target demo_tutorial_indices_base +[ 83%] Built target demo_dox_misc_enumerate_strings make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake --color= -[ 84%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_banded +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_banded.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/depend +[ 83%] Built target demo_tutorial_iterators_assignment_1_solution +[ 83%] Built target demo_unassigned_or_unused_tutorials_custim_io_example1 +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/depend +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/depend make -f demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build.make demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/depend -[ 84%] Built target demo_tutorial_iterators_assignment_4_workshop_solution -[ 84%] Built target demo_howto_align_gaps_clipping make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/depend make -f demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/depend +[ 83%] Built target demo_tutorial_iterators_assignment_3_workshop_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/DependInfo.cmake --color= -[ 84%] Built target demo_tutorial_iterators_sequence_iterator_demo -[ 86%] Built target demo_tutorial_journaled_set_base -[ 86%] Built target demo_tutorial_sequences_example_comparisons make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build +make -f demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build +[ 83%] Built target demo_tutorial_sequence_io_solution1 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/DependInfo.cmake --color= +[ 84%] Built target demo_tutorial_indices_assignment_2 +[ 84%] Built target demo_tutorial_iterators_assignment_4_workshop_solution +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend +[ 84%] Built target demo_howto_align_gaps_clipping make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_sequence_iterator_demo.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_banded make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build.make demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequences_example_comparisons.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build.make demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build.make demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 84%] Built target demo_tutorial_iterators_sequence_iterator_demo make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_basic_simple_type_construction.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build make -f demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build.make demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_journal_string_basic.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_join.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build -[ 86%] Built target demo_tutorial_journaled_set_example_join make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_graph_algorithms_topological_sort.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sequence_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 86%] Built target demo_tutorial_sequence_io_solution3 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_dox_basic_simple_type_construction -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/depend -[ 87%] Built target demo_tutorial_journaled_set_example_journal_string_basic -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/depend -[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step6 -[ 87%] Built target demo_dox_graph_algorithms_topological_sort -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/depend -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/DependInfo.cmake --color= -[ 87%] Built target demo_tutorial_journaled_set_example_online_search_assignment1_hint -[ 87%] Built target demo_tutorial_parsing_command_line_arguments_assignment3_solution -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend -[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_assignment1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/DependInfo.cmake --color= -[ 87%] Built target demo_dox_seq_io_fai_index_example -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_example_online_search_assignment1_hint.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build'. +make -f demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build.make demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment3_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build +[ 84%] Built target demo_tutorial_sequences_example_comparisons make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step6.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_seq_io_fai_index_example.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_assignment4 +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment4.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 86%] Built target demo_tutorial_journaled_set_base +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/depend +[ 87%] Built target demo_dox_basic_simple_type_construction +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/depend +[ 87%] Built target demo_tutorial_journaled_set_example_journal_string_basic make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base.dir/build'. make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_finder.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build -make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/depend +[ 87%] Built target demo_tutorial_journaled_set_example_join +[ 87%] Built target demo_dox_graph_algorithms_topological_sort +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/depend +[ 87%] Built target demo_tutorial_sequence_io_solution3 make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 87%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base -make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/depend -[ 87%] Built target demo_tutorial_sam_and_bam_io_solution3 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/DependInfo.cmake --color= +[ 87%] Built target demo_tutorial_journaled_set_example_online_search_assignment1_hint +[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_assignment1 +[ 87%] Built target demo_dox_seq_io_fai_index_example +[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step6 make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/depend -[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_finder -[ 87%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend -[ 88%] Built target demo_dox_sequence_UNUSED_prefix -make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend +[ 87%] Built target demo_tutorial_parsing_command_line_arguments_assignment3_solution make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5_step3.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/DependInfo.cmake --color= -[ 88%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/depend +[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_finder +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/DependInfo.cmake --color= +[ 87%] Built target demo_tutorial_sam_and_bam_io_solution3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/DependInfo.cmake --color= +[ 87%] Built target demo_tutorial_journaled_set_solution_online_search_assignment4 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/DependInfo.cmake --color= -[ 89%] Built target demo_tutorial_metafunctions_assignment1_solution -[ 89%] Built target demo_tutorial_parsing_command_line_arguments_example_with_struct -[ 89%] Built target demo_unassigned_or_unused_tutorial_file_io_example1 -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/depend +[ 87%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/depend -make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend -make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build.make demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_sequence_UNUSED_prefix.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build +[ 87%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5_step3 +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build.make demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend make -f demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_metafunctions_assignment1_solution.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_metafunctions_base.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_tutorial_file_io_example1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_struct.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build'. -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_seed_and_extend_solution1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build.make demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build +make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_sequence_length.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build +make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_UNUSED_modcomplementdna.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_consensus.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_sam_and_bam_io_solution1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build -[ 89%] Built target demo_tutorial_metafunctions_base -[ 90%] Built target demo_unassigned_or_unused_sequence_length -[ 90%] Built target demo_tutorial_seed_and_extend_solution1 -make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/depend -[ 90%] Built target demo_tutorial_multiple_sequence_alignment_consensus +[ 88%] Built target demo_dox_sequence_UNUSED_prefix +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_modreverse.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Built target demo_tutorial_modifiers_UNUSED_modcomplementdna -make -f demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build.make demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build +[ 88%] Built target demo_tutorial_metafunctions_base make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/depend +[ 89%] Built target demo_tutorial_metafunctions_assignment1_solution +[ 89%] Built target demo_tutorial_parsing_command_line_arguments_example_with_struct +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_sample_seqs.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 89%] Built target demo_unassigned_or_unused_tutorial_file_io_example1 +[ 89%] Built target demo_tutorial_journaled_string_tree_journaled_string_tree_base_assignment1 +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_find_finder_aho_corasick.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 90%] Built target demo_tutorial_modifiers_modreverse -[ 90%] Built target demo_tutorial_modifiers_assignment1 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/DependInfo.cmake --color= make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/depend +[ 89%] Built target demo_tutorial_sam_and_bam_io_solution1 +[ 90%] Built target demo_unassigned_or_unused_sequence_length make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend +[ 90%] Built target demo_tutorial_modifiers_UNUSED_modcomplementdna +[ 90%] Built target demo_tutorial_seed_and_extend_solution1 +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/DependInfo.cmake --color= -[ 90%] Built target demo_tutorial_sam_and_bam_io_solution1 +make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend +[ 90%] Built target demo_tutorial_multiple_sequence_alignment_consensus make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_basics_strings.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/depend -[ 90%] Built target demo_unassigned_or_unused_sample_seqs +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/DependInfo.cmake --color= -[ 90%] Built target demo_dox_find_finder_aho_corasick -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/depend -make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/depend -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build.make demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_modifiers_modview.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend +[ 90%] Built target demo_tutorial_modifiers_assignment1 +[ 90%] Built target demo_tutorial_modifiers_modreverse make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake --color= +[ 90%] Built target demo_dox_find_finder_aho_corasick +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake --color= +[ 90%] Built target demo_unassigned_or_unused_sample_seqs +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/depend make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build +[ 91%] Built target demo_tutorial_modifiers_modview +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build -make -f demos/CMakeFiles/demo_tutorial_basics_strings.dir/build.make demos/CMakeFiles/demo_tutorial_basics_strings.dir/build +make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example_with_modifyString.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_strings.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_basics_strings.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_multiple_sequence_alignment_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build -[ 91%] Built target demo_tutorial_modifiers_modview +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/DependInfo.cmake --color= +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_journaled_set_solution_online_search_assignment2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 91%] Built target demo_tutorial_parsing_command_line_arguments_example_with_modifyString make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build +make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build +make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build'. +make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 91%] Built target demo_tutorial_multiple_sequence_alignment_assignment1 -[ 92%] Built target demo_tutorial_journaled_set_solution_online_search_assignment2 -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/DependInfo.cmake --color= -make -f demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build.make demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build -[ 92%] Built target demo_tutorial_basics_strings -[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 -[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/depend +make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_example_functionality.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/depend -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/depend -make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/depend -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/depend -[ 93%] Built target demo_tutorial_string_sets_example_functionality -make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/DependInfo.cmake --color= -[ 93%] Built target demo_dox_pipe_pool_sorter make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/DependInfo.cmake --color= -[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_dox_pipe_pool_sorter.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build -make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/depend -make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/DependInfo.cmake --color= -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build.make demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build.make demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 91%] Built target demo_tutorial_parsing_command_line_arguments_example_with_modifyString make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build.make demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build -make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_assignment5_solution.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_iterators_assignment_1.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 91%] Built target demo_tutorial_basics_strings make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pairwise_sequence_alignment_assignment5.dir/build'. make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_string_sets_example_functionality_2.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_parsing_command_line_arguments_example1_detailed.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build.make demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build +make -f demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build.make demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build +[ 91%] Built target demo_tutorial_multiple_sequence_alignment_assignment1 +make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/depend +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_a_first_example_basic_code_detailed.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_assignment3.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 94%] Built target demo_tutorial_parsing_command_line_arguments_assignment5_solution -[ 94%] Built target demo_tutorial_pattern_matching_assignment3 +[ 92%] Built target demo_tutorial_journaled_set_solution_online_search_assignment2 make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/depend -[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5 -[ 95%] Built target demo_tutorial_string_sets_example_functionality_2 -[ 95%] Built target demo_tutorial_iterators_assignment_1 -make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend -make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend -[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example1_detailed -make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/DependInfo.cmake --color= -make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend -[ 96%] Built target demo_unassigned_or_unused_bam_print_alignments -make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend -make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/DependInfo.cmake --color= +[ 92%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment3 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_unassigned_or_unused_bam_print_alignments.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/DependInfo.cmake --color= +[ 92%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment2 +[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_assignment1 +make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/depend +[ 93%] Built target demo_tutorial_string_sets_example_functionality +make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/depend +[ 93%] Built target demo_dox_pipe_pool_sorter make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/alf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/alf/CMakeFiles/alf.dir/DependInfo.cmake --color= +[ 93%] Built target demo_tutorial_pairwise_sequence_alignment_alignment_global_overlap +make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake --color= -[ 96%] Built target demo_tutorial_graph_graph_algo_scc -[ 96%] Built target demo_tutorial_a_first_example_basic_code_detailed +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/four2three.dir/DependInfo.cmake --color= +[ 94%] Built target demo_tutorial_parsing_command_line_arguments_assignment5_solution +make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/depend +[ 94%] Built target demo_tutorial_pairwise_sequence_alignment_assignment5 make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/casbar.dir/DependInfo.cmake --color= +make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/depend +[ 94%] Built target demo_tutorial_iterators_assignment_1 +make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/depend +[ 95%] Built target demo_tutorial_string_sets_example_functionality_2 make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/depend +[ 95%] Built target demo_tutorial_a_first_example_basic_code_detailed make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/bs_tools/CMakeFiles/bisar.dir/DependInfo.cmake --color= make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/depend +[ 95%] Built target demo_tutorial_parsing_command_line_arguments_example1_detailed +make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend +make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend +make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/dfi/CMakeFiles/dfi.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/DependInfo.cmake --color= +[ 95%] Built target demo_tutorial_pattern_matching_assignment3 +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake --color= +make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf.dir/DependInfo.cmake --color= +[ 96%] Built target demo_unassigned_or_unused_bam_print_alignments +make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake --color= +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake --color= +make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build +make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake --color= +make -f demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build.make demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build.make demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/alf/CMakeFiles/alf.dir/build.make apps/alf/CMakeFiles/alf.dir/build make -f apps/bs_tools/CMakeFiles/four2three.dir/build.make apps/bs_tools/CMakeFiles/four2three.dir/build -make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/casbar.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_pattern_matching_find_approx.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build -make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build +make -f apps/bs_tools/CMakeFiles/casbar.dir/build.make apps/bs_tools/CMakeFiles/casbar.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/four2three.dir/build'. +make[3]: Nothing to be done for 'demos/CMakeFiles/demo_tutorial_graph_graph_algo_scc.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build +make -f apps/bs_tools/CMakeFiles/bisar.dir/build.make apps/bs_tools/CMakeFiles/bisar.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/bisar.dir/build'. +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake --color= +make -f apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build.make apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/alf/CMakeFiles/alf.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/dfi/CMakeFiles/dfi.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build'. +make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/four2three.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target demo_tutorial_pattern_matching_find_approx +make -f apps/dfi/CMakeFiles/dfi.dir/build.make apps/dfi/CMakeFiles/dfi.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/alf/CMakeFiles/alf.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build.make apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build +make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build make -f apps/gustaf/CMakeFiles/gustaf.dir/build.make apps/gustaf/CMakeFiles/gustaf.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target alf -[ 96%] Built target dfi -make -f apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build.make apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build -[ 96%] Built target casbar -make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/depend -make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/depend -[ 96%] Built target fx_fastq_stats -make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/depend -[ 96%] Built target bisar -make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/depend +make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf.dir/build'. +make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/bisar.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 96%] Built target four2three -[ 96%] Built target fx_bam_coverage -make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/depend -make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/depend +make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build +make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build'. +make[3]: Nothing to be done for 'apps/bs_tools/CMakeFiles/casbar.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/insegt/CMakeFiles/insegt.dir/DependInfo.cmake --color= -make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_variator.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_genome.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_methylation.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_frag_sequencing.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_simulator.dir/DependInfo.cmake --color= -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake --color= -[ 96%] Built target gustaf -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_materializer.dir/DependInfo.cmake --color= -make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend -[ 97%] Built target gustaf_mate_joining -make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/insegt/CMakeFiles/insegt.dir/build.make apps/insegt/CMakeFiles/insegt.dir/build +make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/insegt/CMakeFiles/insegt.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf_mate_joining.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_variator.dir/build.make apps/mason2/CMakeFiles/mason_variator.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_fastq_stats.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'apps/fx_tools/CMakeFiles/fx_bam_coverage.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake --color= +make[3]: Nothing to be done for 'apps/dfi/CMakeFiles/dfi.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_methylation.dir/build.make apps/mason2/CMakeFiles/mason_methylation.dir/build -make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/gustaf/CMakeFiles/gustaf.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_genome.dir/build.make apps/mason2/CMakeFiles/mason_genome.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_variator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_methylation.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/insegt/CMakeFiles/insegt.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build.make apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_tests.dir/build'. +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_genome.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/mason2/CMakeFiles/mason_materializer.dir/build.make apps/mason2/CMakeFiles/mason_materializer.dir/build -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_genome.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target insegt -make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend +make -f apps/mason2/CMakeFiles/mason_simulator.dir/build.make apps/mason2/CMakeFiles/mason_simulator.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_simulator.dir/build'. +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_frag_sequencing.dir/build'. +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_methylation.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_materializer.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_simulator.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 97%] Built target mason_variator -make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build +[ 96%] Built target demo_tutorial_graph_graph_algo_scc +[ 96%] Built target four2three +[ 96%] Built target demo_tutorial_pattern_matching_find_approx +make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/depend +[ 96%] Built target fx_fastq_stats +[ 96%] Built target alf +[ 96%] Built target casbar +make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/depend +make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/depend +[ 96%] Built target bisar +make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/depend +[ 96%] Built target dfi make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/depend -[ 97%] Built target mason_tests -[ 97%] Built target mason_simulator -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build -[ 97%] Built target mason_methylation -[ 97%] Built target mason_frag_sequencing +[ 96%] Built target fx_bam_coverage +[ 97%] Built target gustaf_mate_joining make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/depend -make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_splicing.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/depend make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake --color= -[ 97%] Built target mason_materializer -[ 97%] Built target mason_genome +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_tests.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/micro_razers/CMakeFiles/micro_razers.dir/build'. -make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2 /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/mason2/CMakeFiles/mason_splicing.dir/DependInfo.cmake --color= +[ 97%] Built target gustaf +[ 97%] Built target insegt make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake --color= +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/micro_razers/CMakeFiles/micro_razers.dir/DependInfo.cmake --color= +[ 97%] Built target mason_methylation make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/DependInfo.cmake --color= +[ 97%] Built target mason_frag_sequencing +[ 97%] Built target mason_variator +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/DependInfo.cmake --color= +[ 97%] Built target mason_genome +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/ngs_roi/CMakeFiles/bam2roi.dir/DependInfo.cmake --color= -[ 98%] Built target mason_splicing -[ 98%] Built target micro_razers +[ 97%] Built target mason_simulator +[ 97%] Built target mason_materializer make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build +make -f apps/mason2/CMakeFiles/mason_tests.dir/build.make apps/mason2/CMakeFiles/mason_tests.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/mason2/CMakeFiles/mason_splicing.dir/build.make apps/mason2/CMakeFiles/mason_splicing.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build.make apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -make[3]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build'. +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_tests.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/mason2/CMakeFiles/mason_splicing.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_plot_thumbnails.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make -f apps/micro_razers/CMakeFiles/micro_razers.dir/build.make apps/micro_razers/CMakeFiles/micro_razers.dir/build +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build.make apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build +make -f apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build.make apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/ngs_roi/CMakeFiles/bam2roi.dir/build.make apps/ngs_roi/CMakeFiles/bam2roi.dir/build make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/pair_align/lib/CMakeFiles/pair_align_lib.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[ 98%] Built target roi_plot_thumbnails +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/micro_razers/CMakeFiles/micro_razers.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 97%] Built target roi_plot_thumbnails +[ 98%] Built target mason_splicing +make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +make[3]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/roi_feature_projection.dir/build'. +make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' +[ 98%] Built target mason_tests make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make[3]: Nothing to be done for 'apps/ngs_roi/CMakeFiles/bam2roi.dir/build'. make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' -[100%] Built target roi_feature_projection -[100%] Built target pair_align_lib +[ 98%] Built target pair_align_lib make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/depend +[ 98%] Built target micro_razers make[3]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' cd /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/seqan2-2.4.0+dfsg /build/seqan2-2.4.0+dfsg/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/apps/pair_align/CMakeFiles/pair_align.dir/DependInfo.cmake --color= +[100%] Built target roi_feature_projection [100%] Built target bam2roi make[3]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' make -f apps/pair_align/CMakeFiles/pair_align.dir/build.make apps/pair_align/CMakeFiles/pair_align.dir/build @@ -118595,10 +118665,10 @@ /usr/bin/cmake -E cmake_progress_start /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' dh_auto_test - cd obj-i686-linux-gnu && make -j10 test ARGS\+=-j10 + cd obj-i686-linux-gnu && make -j18 test ARGS\+=-j18 make[1]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process -j10 +/usr/bin/ctest --force-new-ctest-process -j18 Test project /build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu Start 1: test_test_align Start 2: test_test_align_simd_global_equal_length @@ -118610,216 +118680,216 @@ Start 8: test_test_align_parallel_interface Start 9: test_test_align_parallel_algorithm Start 10: test_test_align_profile - 1/107 Test #6: test_test_align_extend ............................. Passed 0.03 sec Start 11: test_test_align_split - 2/107 Test #1: test_test_align .................................... Passed 0.06 sec Start 12: test_test_alignment_free - 3/107 Test #4: test_test_align_simd_local_equal_length ............ Passed 0.15 sec Start 13: test_test_arg_parse - 4/107 Test #5: test_test_align_simd_local_variable_length ......... Passed 0.28 sec Start 14: test_test_arg_parse_version_check - 5/107 Test #10: test_test_align_profile ............................ Passed 0.26 sec Start 15: test_test_bam_io - 6/107 Test #2: test_test_align_simd_global_equal_length ........... Passed 0.42 sec Start 16: test_test_basic_exception - 7/107 Test #3: test_test_align_simd_global_variable_length ........ Passed 0.56 sec Start 17: test_test_basic_metaprogramming - 8/107 Test #7: test_align_parallel_data_structures ................ Passed 0.54 sec Start 18: test_test_basic_fundamental - 9/107 Test #8: test_test_align_parallel_interface ................. Passed 0.55 sec + 1/107 Test #1: test_test_align .................................... Passed 0.04 sec Start 19: test_test_basic_concept - 10/107 Test #9: test_test_align_parallel_algorithm ................. Passed 0.68 sec + 2/107 Test #4: test_test_align_simd_local_equal_length ............ Passed 0.04 sec Start 20: test_test_basic_alphabet - 11/107 Test #11: test_test_align_split .............................. Passed 0.72 sec + 3/107 Test #5: test_test_align_simd_local_variable_length ......... Passed 0.04 sec Start 21: test_test_basic_aggregate - 12/107 Test #13: test_test_arg_parse ................................ Passed 0.49 sec + 4/107 Test #6: test_test_align_extend ............................. Passed 0.04 sec Start 22: test_test_basic_allocator - 13/107 Test #14: test_test_arg_parse_version_check .................. Passed 0.49 sec + 5/107 Test #10: test_test_align_profile ............................ Passed 0.03 sec Start 23: test_test_basic_parallelism - 14/107 Test #16: test_test_basic_exception .......................... Passed 0.35 sec + 6/107 Test #11: test_test_align_split .............................. Passed 0.04 sec Start 24: test_test_basic_math - 15/107 Test #17: test_test_basic_metaprogramming .................... Passed 0.48 sec + 7/107 Test #13: test_test_arg_parse ................................ Passed 0.03 sec Start 25: test_test_basic_smart_pointer - 16/107 Test #18: test_test_basic_fundamental ........................ Passed 0.61 sec + 8/107 Test #16: test_test_basic_exception .......................... Passed 0.02 sec Start 26: test_test_basic_container - 17/107 Test #19: test_test_basic_concept ............................ Passed 0.61 sec + 9/107 Test #17: test_test_basic_metaprogramming .................... Passed 0.02 sec Start 27: test_test_basic_proxy - 18/107 Test #20: test_test_basic_alphabet ........................... Passed 0.70 sec + 10/107 Test #18: test_test_basic_fundamental ........................ Passed 0.02 sec Start 28: test_test_basic_iterator - 19/107 Test #21: test_test_basic_aggregate .......................... Passed 0.80 sec + 11/107 Test #19: test_test_basic_concept ............................ Passed 0.02 sec Start 29: test_test_bed_io - 20/107 Test #22: test_test_basic_allocator .......................... Passed 0.80 sec + 12/107 Test #20: test_test_basic_alphabet ........................... Passed 0.02 sec Start 30: test_blast - 21/107 Test #23: test_test_basic_parallelism ........................ Passed 0.80 sec + 13/107 Test #21: test_test_basic_aggregate .......................... Passed 0.02 sec Start 31: test_test_consensus - 22/107 Test #12: test_test_alignment_free ........................... Passed 1.69 sec + 14/107 Test #22: test_test_basic_allocator .......................... Passed 0.02 sec Start 32: test_test_consensus_v2 - 23/107 Test #24: test_test_basic_math ............................... Passed 0.92 sec + 15/107 Test #23: test_test_basic_parallelism ........................ Passed 0.02 sec Start 33: test_test_find - 24/107 Test #25: test_test_basic_smart_pointer ...................... Passed 0.92 sec + 16/107 Test #24: test_test_basic_math ............................... Passed 0.02 sec Start 34: test_test_gff_io - 25/107 Test #26: test_test_basic_container .......................... Passed 0.91 sec + 17/107 Test #25: test_test_basic_smart_pointer ...................... Passed 0.02 sec Start 35: test_test_graph_algorithms - 26/107 Test #27: test_test_basic_proxy .............................. Passed 0.90 sec + 18/107 Test #26: test_test_basic_container .......................... Passed 0.02 sec Start 36: test_test_graph_align - 27/107 Test #28: test_test_basic_iterator ........................... Passed 0.92 sec + 19/107 Test #2: test_test_align_simd_global_equal_length ........... Passed 0.08 sec Start 37: test_test_graph_msa - 28/107 Test #29: test_test_bed_io ................................... Passed 1.05 sec + 20/107 Test #3: test_test_align_simd_global_variable_length ........ Passed 0.08 sec Start 38: test_test_graph_types_property_map - 29/107 Test #30: test_blast ......................................... Passed 1.06 sec + 21/107 Test #7: test_align_parallel_data_structures ................ Passed 0.08 sec Start 39: test_test_graph_types_derived - 30/107 Test #31: test_test_consensus ................................ Passed 1.01 sec + 22/107 Test #14: test_test_arg_parse_version_check .................. Passed 0.06 sec Start 40: test_test_graph_types_iterators - 31/107 Test #32: test_test_consensus_v2 ............................. Passed 0.91 sec + 23/107 Test #27: test_test_basic_proxy .............................. Passed 0.03 sec Start 41: test_test_graph_types_types - 32/107 Test #33: test_test_find ..................................... Passed 0.81 sec + 24/107 Test #28: test_test_basic_iterator ........................... Passed 0.03 sec Start 42: test_test_graph_types_utils - 33/107 Test #34: test_test_gff_io ................................... Passed 0.84 sec + 25/107 Test #29: test_test_bed_io ................................... Passed 0.03 sec Start 43: test_test_index_creation - 34/107 Test #35: test_test_graph_algorithms ......................... Passed 0.84 sec + 26/107 Test #34: test_test_gff_io ................................... Passed 0.02 sec Start 44: test_test_index_crosscompare_char - 35/107 Test #36: test_test_graph_align .............................. Passed 0.84 sec + 27/107 Test #30: test_blast ......................................... Passed 0.03 sec Start 45: test_test_index_crosscompare_char_dfi - 36/107 Test #37: test_test_graph_msa ................................ Passed 0.85 sec + 28/107 Test #31: test_test_consensus ................................ Passed 0.04 sec Start 46: test_test_index_crosscompare_dna - 37/107 Test #38: test_test_graph_types_property_map ................. Passed 0.85 sec + 29/107 Test #35: test_test_graph_algorithms ......................... Passed 0.03 sec Start 47: test_test_index_crosscompare_dna_dfi - 38/107 Test #39: test_test_graph_types_derived ...................... Passed 0.85 sec + 30/107 Test #36: test_test_graph_align .............................. Passed 0.03 sec Start 48: test_test_index_qgram - 39/107 Test #40: test_test_graph_types_iterators .................... Passed 0.83 sec + 31/107 Test #38: test_test_graph_types_property_map ................. Passed 0.02 sec Start 49: test_test_index_sa_bwtwalk - 40/107 Test #41: test_test_graph_types_types ........................ Passed 0.87 sec + 32/107 Test #39: test_test_graph_types_derived ...................... Passed 0.03 sec Start 50: test_test_index_shapes - 41/107 Test #42: test_test_graph_types_utils ........................ Passed 0.73 sec + 33/107 Test #40: test_test_graph_types_iterators .................... Passed 0.03 sec Start 51: test_test_index_drawing - 42/107 Test #43: test_test_index_creation ........................... Passed 0.62 sec + 34/107 Test #41: test_test_graph_types_types ........................ Passed 0.03 sec Start 52: test_test_index_fm_rank_dictionary - 43/107 Test #44: test_test_index_crosscompare_char .................. Passed 0.49 sec + 35/107 Test #42: test_test_graph_types_utils ........................ Passed 0.03 sec Start 53: test_test_index_fm_sparse_string - 44/107 Test #45: test_test_index_crosscompare_char_dfi .............. Passed 0.35 sec + 36/107 Test #44: test_test_index_crosscompare_char .................. Passed 0.03 sec Start 54: test_test_index_base - 45/107 Test #46: test_test_index_crosscompare_dna ................... Passed 0.22 sec + 37/107 Test #45: test_test_index_crosscompare_char_dfi .............. Passed 0.04 sec Start 55: test_test_index_fm - 46/107 Test #47: test_test_index_crosscompare_dna_dfi ............... Passed 0.13 sec + 38/107 Test #46: test_test_index_crosscompare_dna ................... Passed 0.04 sec Start 56: test_test_index_bifm - 47/107 Test #48: test_test_index_qgram .............................. Passed 0.13 sec + 39/107 Test #47: test_test_index_crosscompare_dna_dfi ............... Passed 0.04 sec Start 57: test_test_index_vstree - 48/107 Test #50: test_test_index_shapes ............................. Passed 0.05 sec + 40/107 Test #48: test_test_index_qgram .............................. Passed 0.05 sec Start 58: test_test_index_view - 49/107 Test #51: test_test_index_drawing ............................ Passed 0.05 sec + 41/107 Test #50: test_test_index_shapes ............................. Passed 0.06 sec Start 59: test_test_index_finder - 50/107 Test #53: test_test_index_fm_sparse_string ................... Passed 0.06 sec + 42/107 Test #51: test_test_index_drawing ............................ Passed 0.06 sec Start 60: test_test_find_backtracking - 51/107 Test #58: test_test_index_view ............................... Passed 0.05 sec + 43/107 Test #8: test_test_align_parallel_interface ................. Passed 0.18 sec Start 61: test_test_index_repeats - 52/107 Test #49: test_test_index_sa_bwtwalk ......................... Passed 0.17 sec + 44/107 Test #53: test_test_index_fm_sparse_string ................... Passed 0.10 sec Start 62: test_test_journaled_set - 53/107 Test #60: test_test_find_backtracking ........................ Passed 0.09 sec + 45/107 Test #58: test_test_index_view ............................... Passed 0.07 sec Start 63: test_test_journaled_string_tree - 54/107 Test #62: test_test_journaled_set ............................ Passed 0.06 sec + 46/107 Test #60: test_test_find_backtracking ........................ Passed 0.06 sec Start 64: test_test_delta_map - 55/107 Test #63: test_test_journaled_string_tree .................... Passed 0.07 sec + 47/107 Test #49: test_test_index_sa_bwtwalk ......................... Passed 0.14 sec Start 65: test_journaled_string_tree_traverser - 56/107 Test #64: test_test_delta_map ................................ Passed 0.05 sec + 48/107 Test #62: test_test_journaled_set ............................ Passed 0.03 sec Start 66: test_journaled_string_tree_find - 57/107 Test #61: test_test_index_repeats ............................ Passed 0.25 sec + 49/107 Test #63: test_test_journaled_string_tree .................... Passed 0.04 sec Start 67: test_test_map - 58/107 Test #65: test_journaled_string_tree_traverser ............... Passed 0.27 sec + 50/107 Test #64: test_test_delta_map ................................ Passed 0.04 sec Start 68: test_test_misc - 59/107 Test #68: test_test_misc ..................................... Passed 0.03 sec + 51/107 Test #68: test_test_misc ..................................... Passed 0.01 sec Start 69: test_test_modifier - 60/107 Test #69: test_test_modifier ................................. Passed 0.10 sec + 52/107 Test #61: test_test_index_repeats ............................ Passed 0.18 sec Start 70: test_test_modifier_cyclic_shape - 61/107 Test #70: test_test_modifier_cyclic_shape .................... Passed 0.04 sec + 53/107 Test #43: test_test_index_creation ........................... Passed 0.29 sec Start 71: test_test_multiple_translation_units - 62/107 Test #71: test_test_multiple_translation_units ............... Passed 0.03 sec + 54/107 Test #69: test_test_modifier ................................. Passed 0.11 sec Start 72: test_test_parallel - 63/107 Test #59: test_test_index_finder ............................. Passed 2.79 sec + 55/107 Test #70: test_test_modifier_cyclic_shape .................... Passed 0.04 sec Start 73: test_test_parse_lm - 64/107 Test #73: test_test_parse_lm ................................. Passed 0.03 sec + 56/107 Test #9: test_test_align_parallel_algorithm ................. Passed 0.43 sec Start 74: test_test_pipe - 65/107 Test #52: test_test_index_fm_rank_dictionary ................. Passed 3.10 sec + 57/107 Test #71: test_test_multiple_translation_units ............... Passed 0.07 sec Start 75: test_test_platform - 66/107 Test #75: test_test_platform ................................. Passed 0.03 sec + 58/107 Test #73: test_test_parse_lm ................................. Passed 0.06 sec Start 76: test_test_random - 67/107 Test #76: test_test_random ................................... Passed 0.04 sec + 59/107 Test #32: test_test_consensus_v2 ............................. Passed 0.41 sec Start 77: test_test_realign - 68/107 Test #67: test_test_map ...................................... Passed 2.94 sec + 60/107 Test #75: test_test_platform ................................. Passed 0.04 sec Start 78: test_reduced_aminoacid - 69/107 Test #78: test_reduced_aminoacid ............................. Passed 0.10 sec + 61/107 Test #37: test_test_graph_msa ................................ Passed 0.43 sec Start 79: test_test_rna_io - 70/107 Test #79: test_test_rna_io ................................... Passed 0.05 sec + 62/107 Test #65: test_journaled_string_tree_traverser ............... Passed 0.27 sec Start 80: test_test_roi_io - 71/107 Test #80: test_test_roi_io ................................... Passed 0.03 sec + 63/107 Test #76: test_test_random ................................... Passed 0.07 sec Start 81: test_test_score - 72/107 Test #81: test_test_score .................................... Passed 0.07 sec + 64/107 Test #80: test_test_roi_io ................................... Passed 0.02 sec Start 82: test_test_seeds_combination - 73/107 Test #82: test_test_seeds_combination ........................ Passed 0.04 sec + 65/107 Test #82: test_test_seeds_combination ........................ Passed 0.01 sec Start 83: test_test_seeds_extension - 74/107 Test #83: test_test_seeds_extension .......................... Passed 0.03 sec + 66/107 Test #81: test_test_score .................................... Passed 0.02 sec Start 84: test_test_seeds_global_chaining - 75/107 Test #84: test_test_seeds_global_chaining .................... Passed 0.03 sec + 67/107 Test #83: test_test_seeds_extension .......................... Passed 0.01 sec Start 85: test_test_seeds_seed_base - 76/107 Test #85: test_test_seeds_seed_base .......................... Passed 0.02 sec + 68/107 Test #84: test_test_seeds_global_chaining .................... Passed 0.02 sec Start 86: test_test_seeds_seed_chained - 77/107 Test #86: test_test_seeds_seed_chained ....................... Passed 0.02 sec + 69/107 Test #78: test_reduced_aminoacid ............................. Passed 0.08 sec Start 87: test_test_seeds_seed_diagonal - 78/107 Test #87: test_test_seeds_seed_diagonal ...................... Passed 0.01 sec + 70/107 Test #79: test_test_rna_io ................................... Passed 0.08 sec Start 88: test_test_seeds_seed_set_base - 79/107 Test #88: test_test_seeds_seed_set_base ...................... Passed 0.03 sec + 71/107 Test #85: test_test_seeds_seed_base .......................... Passed 0.04 sec Start 89: test_test_seeds_seed_set_unordered - 80/107 Test #89: test_test_seeds_seed_set_unordered ................. Passed 0.02 sec + 72/107 Test #86: test_test_seeds_seed_chained ....................... Passed 0.04 sec Start 90: test_test_seeds_align_banded_chain_impl - 81/107 Test #90: test_test_seeds_align_banded_chain_impl ............ Passed 0.16 sec + 73/107 Test #33: test_test_find ..................................... Passed 0.55 sec Start 91: test_test_seeds_banded_chain_alignment_interface - 82/107 Test #77: test_test_realign .................................. Passed 0.87 sec + 74/107 Test #87: test_test_seeds_seed_diagonal ...................... Passed 0.05 sec Start 92: test_test_seq_io - 83/107 Test #91: test_test_seeds_banded_chain_alignment_interface ... Passed 0.18 sec + 75/107 Test #88: test_test_seeds_seed_set_base ...................... Passed 0.06 sec Start 93: test_test_sequence - 84/107 Test #93: test_test_sequence ................................. Passed 0.08 sec + 76/107 Test #89: test_test_seeds_seed_set_unordered ................. Passed 0.06 sec Start 94: test_test_sequence_v2 - 85/107 Test #57: test_test_index_vstree ............................. Passed 4.43 sec + 77/107 Test #91: test_test_seeds_banded_chain_alignment_interface ... Passed 0.05 sec Start 95: test_test_stringset_v2 - 86/107 Test #95: test_test_stringset_v2 ............................. Passed 0.12 sec + 78/107 Test #90: test_test_seeds_align_banded_chain_impl ............ Passed 0.07 sec Start 96: test_test_sequence_journaled - 87/107 Test #96: test_test_sequence_journaled ....................... Passed 0.05 sec + 79/107 Test #96: test_test_sequence_journaled ....................... Passed 0.01 sec Start 97: test_test_simd_vector - 88/107 Test #97: test_test_simd_vector .............................. Passed 0.03 sec + 80/107 Test #97: test_test_simd_vector .............................. Passed 0.00 sec Start 98: test_test_simple_intervals_io - 89/107 Test #98: test_test_simple_intervals_io ...................... Passed 0.04 sec + 81/107 Test #98: test_test_simple_intervals_io ...................... Passed 0.01 sec Start 99: test_test_statistics - 90/107 Test #74: test_test_pipe ..................................... Passed 1.89 sec + 82/107 Test #95: test_test_stringset_v2 ............................. Passed 0.04 sec Start 100: test_test_store - 91/107 Test #92: test_test_seq_io ................................... Passed 0.91 sec + 83/107 Test #99: test_test_statistics ............................... Passed 0.02 sec Start 101: test_test_stream - 92/107 Test #99: test_test_statistics ............................... Passed 0.26 sec + 84/107 Test #93: test_test_sequence ................................. Passed 0.15 sec Start 102: test_test_find_swift - 93/107 Test #102: test_test_find_swift ............................... Passed 0.03 sec + 85/107 Test #102: test_test_find_swift ............................... Passed 0.01 sec Start 103: test_test_tabix_io - 94/107 Test #103: test_test_tabix_io ................................. Passed 0.17 sec + 86/107 Test #77: test_test_realign .................................. Passed 0.38 sec Start 104: test_translation - 95/107 Test #104: test_translation ................................... Passed 0.70 sec + 87/107 Test #103: test_test_tabix_io ................................. Passed 0.10 sec Start 105: test_ucsc_io - 96/107 Test #105: test_ucsc_io ....................................... Passed 0.04 sec + 88/107 Test #105: test_ucsc_io ....................................... Passed 0.01 sec Start 106: test_test_vcf_io - 97/107 Test #106: test_test_vcf_io ................................... Passed 0.05 sec + 89/107 Test #106: test_test_vcf_io ................................... Passed 0.01 sec Start 107: test_test_funcs_param_chooser - 98/107 Test #107: test_test_funcs_param_chooser ...................... Passed 0.03 sec - 99/107 Test #72: test_test_parallel ................................. Passed 6.32 sec -100/107 Test #54: test_test_index_base ............................... Passed 7.19 sec -101/107 Test #100: test_test_store .................................... Passed 2.51 sec -102/107 Test #94: test_test_sequence_v2 .............................. Passed 3.68 sec -103/107 Test #55: test_test_index_fm ................................. Passed 10.89 sec -104/107 Test #101: test_test_stream ................................... Passed 12.96 sec -105/107 Test #56: test_test_index_bifm ............................... Passed 32.73 sec -106/107 Test #15: test_test_bam_io ................................... Passed 41.08 sec -107/107 Test #66: test_journaled_string_tree_find .................... Passed 40.39 sec + 90/107 Test #92: test_test_seq_io ................................... Passed 0.33 sec + 91/107 Test #107: test_test_funcs_param_chooser ...................... Passed 0.03 sec + 92/107 Test #67: test_test_map ...................................... Passed 0.84 sec + 93/107 Test #52: test_test_index_fm_rank_dictionary ................. Passed 1.15 sec + 94/107 Test #59: test_test_index_finder ............................. Passed 1.25 sec + 95/107 Test #74: test_test_pipe ..................................... Passed 1.10 sec + 96/107 Test #104: test_translation ................................... Passed 0.69 sec + 97/107 Test #100: test_test_store .................................... Passed 0.88 sec + 98/107 Test #12: test_test_alignment_free ........................... Passed 1.73 sec + 99/107 Test #94: test_test_sequence_v2 .............................. Passed 1.30 sec +100/107 Test #57: test_test_index_vstree ............................. Passed 2.22 sec +101/107 Test #54: test_test_index_base ............................... Passed 2.90 sec +102/107 Test #101: test_test_stream ................................... Passed 2.45 sec +103/107 Test #72: test_test_parallel ................................. Passed 4.36 sec +104/107 Test #55: test_test_index_fm ................................. Passed 4.96 sec +105/107 Test #66: test_journaled_string_tree_find .................... Passed 19.16 sec +106/107 Test #56: test_test_index_bifm ............................... Passed 19.91 sec +107/107 Test #15: test_test_bam_io ................................... Passed 20.47 sec 100% tests passed, 0 tests failed out of 107 -Total Test time (real) = 44.50 sec +Total Test time (real) = 20.51 sec make[1]: Leaving directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' - rm -fr -- /tmp/dh-xdg-rundir-z6TAODMr + rm -fr -- /tmp/dh-xdg-rundir-eFWEWcgQ create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/seqan-apps.substvars debian/libseqan2-dev.substvars @@ -118829,7 +118899,7 @@ make[1]: Entering directory '/build/seqan2-2.4.0+dfsg' dh_auto_install --indep -B build --destdir=/build/seqan2-2.4.0+dfsg/debian/libseqan2-dev/ install -d /build/seqan2-2.4.0\+dfsg/debian/libseqan2-dev - cd build && make -j10 install DESTDIR=/build/seqan2-2.4.0\+dfsg/debian/libseqan2-dev AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd build && make -j18 install DESTDIR=/build/seqan2-2.4.0\+dfsg/debian/libseqan2-dev AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/seqan2-2.4.0+dfsg/build' /usr/bin/cmake -S/build/seqan2-2.4.0+dfsg -B/build/seqan2-2.4.0+dfsg/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -119578,7 +119648,7 @@ make[1]: Leaving directory '/build/seqan2-2.4.0+dfsg' dh_auto_install -Nlibseqan2-dev install -d /build/seqan2-2.4.0\+dfsg/debian/tmp - cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/seqan2-2.4.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j18 install DESTDIR=/build/seqan2-2.4.0\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/seqan2-2.4.0+dfsg -B/build/seqan2-2.4.0+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -119816,10 +119886,10 @@ chmod -R u\+rw,go=rX debian/libseqan2-dev/usr/share/doc install -p -m0644 debian/copyright debian/libseqan2-dev/usr/share/doc/libseqan2-dev/copyright dh_installchangelogs - install -p -m0644 debian/changelog debian/seqan-apps/usr/share/doc/seqan-apps/changelog.Debian - install -p -m0644 ./CHANGELOG.rst debian/seqan-apps/usr/share/doc/seqan-apps/changelog install -p -m0644 debian/changelog debian/libseqan2-dev/usr/share/doc/libseqan2-dev/changelog.Debian install -p -m0644 ./CHANGELOG.rst debian/libseqan2-dev/usr/share/doc/libseqan2-dev/changelog + install -p -m0644 debian/changelog debian/seqan-apps/usr/share/doc/seqan-apps/changelog.Debian + install -p -m0644 ./CHANGELOG.rst debian/seqan-apps/usr/share/doc/seqan-apps/changelog rm -f debian/libseqan2-dev.debhelper.log debian/rules override_dh_installman-arch make[1]: Entering directory '/build/seqan2-2.4.0+dfsg' @@ -119879,38 +119949,38 @@ man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/insegt.1 debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/mason_genome.1 debian/seqan-apps/usr/share/man/man1/mason_materializer.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/mason_methylation.1 debian/seqan-apps/usr/share/man/man1/micro_razers.1 + man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/pair_align.1 debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1 debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/razers.1 debian/seqan-apps/usr/share/man/man1/razers3.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/sak.1 debian/seqan-apps/usr/share/man/man1/seqan_tcoffee.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/snp_store.1 debian/seqan-apps/usr/share/man/man1/stellar.1 man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/tree_recon.1 - man-recode --to-code UTF-8 --suffix .dh-new debian/seqan-apps/usr/share/man/man1/pair_align.1 debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 mv debian/seqan-apps/usr/share/man/man1/tree_recon.1.dh-new debian/seqan-apps/usr/share/man/man1/tree_recon.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/tree_recon.1 - mv debian/seqan-apps/usr/share/man/man1/pair_align.1.dh-new debian/seqan-apps/usr/share/man/man1/pair_align.1 - mv debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 - chmod 0644 -- debian/seqan-apps/usr/share/man/man1/pair_align.1 debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 - mv debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1 - mv debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1 - chmod 0644 -- debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1 debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1 - mv debian/seqan-apps/usr/share/man/man1/mason_methylation.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_methylation.1 - mv debian/seqan-apps/usr/share/man/man1/micro_razers.1.dh-new debian/seqan-apps/usr/share/man/man1/micro_razers.1 - chmod 0644 -- debian/seqan-apps/usr/share/man/man1/mason_methylation.1 debian/seqan-apps/usr/share/man/man1/micro_razers.1 - mv debian/seqan-apps/usr/share/man/man1/insegt.1.dh-new debian/seqan-apps/usr/share/man/man1/insegt.1 - mv debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1 - chmod 0644 -- debian/seqan-apps/usr/share/man/man1/insegt.1 debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1 mv debian/seqan-apps/usr/share/man/man1/alf.1.dh-new debian/seqan-apps/usr/share/man/man1/alf.1 mv debian/seqan-apps/usr/share/man/man1/gustaf.1.dh-new debian/seqan-apps/usr/share/man/man1/gustaf.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/alf.1 debian/seqan-apps/usr/share/man/man1/gustaf.1 + mv debian/seqan-apps/usr/share/man/man1/mason_methylation.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_methylation.1 + mv debian/seqan-apps/usr/share/man/man1/micro_razers.1.dh-new debian/seqan-apps/usr/share/man/man1/micro_razers.1 + chmod 0644 -- debian/seqan-apps/usr/share/man/man1/mason_methylation.1 debian/seqan-apps/usr/share/man/man1/micro_razers.1 mv debian/seqan-apps/usr/share/man/man1/snp_store.1.dh-new debian/seqan-apps/usr/share/man/man1/snp_store.1 mv debian/seqan-apps/usr/share/man/man1/stellar.1.dh-new debian/seqan-apps/usr/share/man/man1/stellar.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/snp_store.1 debian/seqan-apps/usr/share/man/man1/stellar.1 + mv debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1 + mv debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1 + chmod 0644 -- debian/seqan-apps/usr/share/man/man1/rabema_evaluate.1 debian/seqan-apps/usr/share/man/man1/rabema_prepare_sam.1 mv debian/seqan-apps/usr/share/man/man1/mason_genome.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_genome.1 mv debian/seqan-apps/usr/share/man/man1/mason_materializer.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_materializer.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/mason_genome.1 debian/seqan-apps/usr/share/man/man1/mason_materializer.1 + mv debian/seqan-apps/usr/share/man/man1/insegt.1.dh-new debian/seqan-apps/usr/share/man/man1/insegt.1 + mv debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1.dh-new debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1 + chmod 0644 -- debian/seqan-apps/usr/share/man/man1/insegt.1 debian/seqan-apps/usr/share/man/man1/mason_frag_sequencing.1 mv debian/seqan-apps/usr/share/man/man1/razers.1.dh-new debian/seqan-apps/usr/share/man/man1/razers.1 mv debian/seqan-apps/usr/share/man/man1/razers3.1.dh-new debian/seqan-apps/usr/share/man/man1/razers3.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/razers.1 debian/seqan-apps/usr/share/man/man1/razers3.1 + mv debian/seqan-apps/usr/share/man/man1/pair_align.1.dh-new debian/seqan-apps/usr/share/man/man1/pair_align.1 + mv debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1.dh-new debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 + chmod 0644 -- debian/seqan-apps/usr/share/man/man1/pair_align.1 debian/seqan-apps/usr/share/man/man1/rabema_build_gold_standard.1 mv debian/seqan-apps/usr/share/man/man1/sak.1.dh-new debian/seqan-apps/usr/share/man/man1/sak.1 mv debian/seqan-apps/usr/share/man/man1/seqan_tcoffee.1.dh-new debian/seqan-apps/usr/share/man/man1/seqan_tcoffee.1 chmod 0644 -- debian/seqan-apps/usr/share/man/man1/sak.1 debian/seqan-apps/usr/share/man/man1/seqan_tcoffee.1 @@ -119921,44 +119991,44 @@ debian/rules override_dh_link-arch make[1]: Entering directory '/build/seqan2-2.4.0+dfsg' dh_link --arch + rm -f debian/seqan-apps/usr/bin/insegt + ln -s ../lib/seqan/bin/insegt debian/seqan-apps/usr/bin/insegt + rm -f debian/seqan-apps/usr/bin/seqan_tcoffee + ln -s ../lib/seqan/bin/seqan_tcoffee debian/seqan-apps/usr/bin/seqan_tcoffee rm -f debian/seqan-apps/usr/bin/rabema_build_gold_standard ln -s ../lib/seqan/bin/rabema_build_gold_standard debian/seqan-apps/usr/bin/rabema_build_gold_standard - rm -f debian/seqan-apps/usr/bin/gustaf - ln -s ../lib/seqan/bin/gustaf debian/seqan-apps/usr/bin/gustaf - rm -f debian/seqan-apps/usr/bin/snp_store - ln -s ../lib/seqan/bin/snp_store debian/seqan-apps/usr/bin/snp_store + rm -f debian/seqan-apps/usr/bin/sak + ln -s ../lib/seqan/bin/sak debian/seqan-apps/usr/bin/sak + rm -f debian/seqan-apps/usr/bin/razers3 + ln -s ../lib/seqan/bin/razers3 debian/seqan-apps/usr/bin/razers3 rm -f debian/seqan-apps/usr/bin/razers ln -s ../lib/seqan/bin/razers debian/seqan-apps/usr/bin/razers - rm -f debian/seqan-apps/usr/bin/mason_frag_sequencing - ln -s ../lib/seqan/bin/mason_frag_sequencing debian/seqan-apps/usr/bin/mason_frag_sequencing - rm -f debian/seqan-apps/usr/bin/seqan_tcoffee - ln -s ../lib/seqan/bin/seqan_tcoffee debian/seqan-apps/usr/bin/seqan_tcoffee - rm -f debian/seqan-apps/usr/bin/mason_genome - ln -s ../lib/seqan/bin/mason_genome debian/seqan-apps/usr/bin/mason_genome - rm -f debian/seqan-apps/usr/bin/insegt - ln -s ../lib/seqan/bin/insegt debian/seqan-apps/usr/bin/insegt - rm -f debian/seqan-apps/usr/bin/mason_materializer - ln -s ../lib/seqan/bin/mason_materializer debian/seqan-apps/usr/bin/mason_materializer rm -f debian/seqan-apps/usr/bin/stellar ln -s ../lib/seqan/bin/stellar debian/seqan-apps/usr/bin/stellar - rm -f debian/seqan-apps/usr/bin/rabema_prepare_sam - ln -s ../lib/seqan/bin/rabema_prepare_sam debian/seqan-apps/usr/bin/rabema_prepare_sam - rm -f debian/seqan-apps/usr/bin/sak - ln -s ../lib/seqan/bin/sak debian/seqan-apps/usr/bin/sak + rm -f debian/seqan-apps/usr/bin/snp_store + ln -s ../lib/seqan/bin/snp_store debian/seqan-apps/usr/bin/snp_store + rm -f debian/seqan-apps/usr/bin/mason_methylation + ln -s ../lib/seqan/bin/mason_methylation debian/seqan-apps/usr/bin/mason_methylation + rm -f debian/seqan-apps/usr/bin/tree_recon + ln -s ../lib/seqan/bin/tree_recon debian/seqan-apps/usr/bin/tree_recon rm -f debian/seqan-apps/usr/bin/alf ln -s ../lib/seqan/bin/alf debian/seqan-apps/usr/bin/alf + rm -f debian/seqan-apps/usr/bin/pair_align + ln -s ../lib/seqan/bin/pair_align debian/seqan-apps/usr/bin/pair_align rm -f debian/seqan-apps/usr/bin/micro_razers ln -s ../lib/seqan/bin/micro_razers debian/seqan-apps/usr/bin/micro_razers - rm -f debian/seqan-apps/usr/bin/razers3 - ln -s ../lib/seqan/bin/razers3 debian/seqan-apps/usr/bin/razers3 + rm -f debian/seqan-apps/usr/bin/rabema_prepare_sam + ln -s ../lib/seqan/bin/rabema_prepare_sam debian/seqan-apps/usr/bin/rabema_prepare_sam rm -f debian/seqan-apps/usr/bin/rabema_evaluate ln -s ../lib/seqan/bin/rabema_evaluate debian/seqan-apps/usr/bin/rabema_evaluate - rm -f debian/seqan-apps/usr/bin/pair_align - ln -s ../lib/seqan/bin/pair_align debian/seqan-apps/usr/bin/pair_align - rm -f debian/seqan-apps/usr/bin/tree_recon - ln -s ../lib/seqan/bin/tree_recon debian/seqan-apps/usr/bin/tree_recon - rm -f debian/seqan-apps/usr/bin/mason_methylation - ln -s ../lib/seqan/bin/mason_methylation debian/seqan-apps/usr/bin/mason_methylation + rm -f debian/seqan-apps/usr/bin/mason_frag_sequencing + ln -s ../lib/seqan/bin/mason_frag_sequencing debian/seqan-apps/usr/bin/mason_frag_sequencing + rm -f debian/seqan-apps/usr/bin/gustaf + ln -s ../lib/seqan/bin/gustaf debian/seqan-apps/usr/bin/gustaf + rm -f debian/seqan-apps/usr/bin/mason_genome + ln -s ../lib/seqan/bin/mason_genome debian/seqan-apps/usr/bin/mason_genome + rm -f debian/seqan-apps/usr/bin/mason_materializer + ln -s ../lib/seqan/bin/mason_materializer debian/seqan-apps/usr/bin/mason_materializer rm -f debian/seqan-apps/usr/bin/yara_mapper ln -s ../lib/seqan/bin/yara_mapper debian/seqan-apps/usr/bin/yara_mapper rm -f debian/seqan-apps/usr/bin/yara_indexer @@ -120015,8 +120085,8 @@ Normalizing debian/seqan-apps/usr/share/doc/seqan-apps/ngs_roi/R/ngsroi_0.1.tar.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/seqan-apps/usr/share/doc/seqan-apps/ngs_roi/R/ngsroi_0.1.zip using File::StripNondeterminism::handlers::zip dh_compress - cd debian/libseqan2-dev cd debian/seqan-apps + cd debian/libseqan2-dev chmod a-x usr/share/doc/libseqan2-dev/changelog usr/share/doc/libseqan2-dev/changelog.Debian gzip -9nf usr/share/doc/libseqan2-dev/changelog usr/share/doc/libseqan2-dev/changelog.Debian chmod a-x usr/share/doc/seqan-apps/alf/README usr/share/doc/seqan-apps/changelog usr/share/doc/seqan-apps/changelog.Debian usr/share/doc/seqan-apps/dfi/README usr/share/doc/seqan-apps/gustaf/README usr/share/doc/seqan-apps/gustaf/example/adeno.fa usr/share/doc/seqan-apps/gustaf/example/adeno_modified.fa usr/share/doc/seqan-apps/insegt/README usr/share/doc/seqan-apps/mason2/README.mason_methylation usr/share/doc/seqan-apps/mason2/README.mason_simulator usr/share/doc/seqan-apps/mason2/README.mason_variator usr/share/doc/seqan-apps/mason2/example/adeno_virus.fa usr/share/doc/seqan-apps/micro_razers/README usr/share/doc/seqan-apps/ngs_roi/README usr/share/doc/seqan-apps/ngs_roi/example/dmel.bed usr/share/doc/seqan-apps/ngs_roi/example/dmel.gtf usr/share/doc/seqan-apps/ngs_roi/example/example.bam usr/share/doc/seqan-apps/rabema/README usr/share/doc/seqan-apps/razers/README usr/share/doc/seqan-apps/razers3/README usr/share/doc/seqan-apps/sgip/example/iso_r01_m200.A00 usr/share/doc/seqan-apps/sgip/example/iso_r01_m200.A01 usr/share/doc/seqan-apps/sgip/example/iso_r01_m200.B00 usr/share/doc/seqan-apps/sgip/example/iso_r01_m200.B01 usr/share/doc/seqan-apps/snp_store/README usr/share/doc/seqan-apps/snp_store/example/exampleGenome.fa usr/share/doc/seqan-apps/stellar/README usr/share/doc/seqan-apps/stellar/example/NC_001474.fasta usr/share/doc/seqan-apps/stellar/example/NC_001477.fasta usr/share/man/man1/alf.1 usr/share/man/man1/gustaf.1 usr/share/man/man1/insegt.1 usr/share/man/man1/mason_frag_sequencing.1 usr/share/man/man1/mason_genome.1 usr/share/man/man1/mason_materializer.1 usr/share/man/man1/mason_methylation.1 usr/share/man/man1/micro_razers.1 usr/share/man/man1/pair_align.1 usr/share/man/man1/rabema_build_gold_standard.1 usr/share/man/man1/rabema_evaluate.1 usr/share/man/man1/rabema_prepare_sam.1 usr/share/man/man1/razers.1 usr/share/man/man1/razers3.1 usr/share/man/man1/sak.1 usr/share/man/man1/seqan_tcoffee.1 usr/share/man/man1/snp_store.1 usr/share/man/man1/stellar.1 usr/share/man/man1/tree_recon.1 @@ -120050,196 +120120,196 @@ dwz -mdebian/seqan-apps/usr/lib/debug/.dwz/i386-linux-gnu/seqan-apps.debug -M/usr/lib/debug/.dwz/i386-linux-gnu/seqan-apps.debug -- debian/seqan-apps/usr/lib/seqan/bin/alf debian/seqan-apps/usr/lib/seqan/bin/bam2roi debian/seqan-apps/usr/lib/seqan/bin/bisar debian/seqan-apps/usr/lib/seqan/bin/casbar debian/seqan-apps/usr/lib/seqan/bin/dfi debian/seqan-apps/usr/lib/seqan/bin/four2three debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage debian/seqan-apps/usr/lib/seqan/bin/gustaf debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining debian/seqan-apps/usr/lib/seqan/bin/insegt debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing debian/seqan-apps/usr/lib/seqan/bin/mason_genome debian/seqan-apps/usr/lib/seqan/bin/mason_materializer debian/seqan-apps/usr/lib/seqan/bin/mason_methylation debian/seqan-apps/usr/lib/seqan/bin/mason_simulator debian/seqan-apps/usr/lib/seqan/bin/mason_splicing debian/seqan-apps/usr/lib/seqan/bin/mason_variator debian/seqan-apps/usr/lib/seqan/bin/micro_razers debian/seqan-apps/usr/lib/seqan/bin/pair_align debian/seqan-apps/usr/lib/seqan/bin/param_chooser debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam debian/seqan-apps/usr/lib/seqan/bin/razers debian/seqan-apps/usr/lib/seqan/bin/razers3 debian/seqan-apps/usr/lib/seqan/bin/rep_sep debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails debian/seqan-apps/usr/lib/seqan/bin/s4_join debian/seqan-apps/usr/lib/seqan/bin/s4_search debian/seqan-apps/usr/lib/seqan/bin/sak debian/seqan-apps/usr/lib/seqan/bin/sam2matrix debian/seqan-apps/usr/lib/seqan/bin/samcat debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee debian/seqan-apps/usr/lib/seqan/bin/seqcons2 debian/seqan-apps/usr/lib/seqan/bin/sgip debian/seqan-apps/usr/lib/seqan/bin/snp_store debian/seqan-apps/usr/lib/seqan/bin/stellar debian/seqan-apps/usr/lib/seqan/bin/tree_recon objcopy --compress-debug-sections debian/seqan-apps/usr/lib/debug/.dwz/i386-linux-gnu/seqan-apps.debug dh_strip -a - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/seqcons2 debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/seqcons2 - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug debian/seqan-apps/usr/lib/seqan/bin/seqcons2 - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/s4_join debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/s4_join - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug debian/seqan-apps/usr/lib/seqan/bin/s4_join - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_methylation debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_methylation - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug debian/seqan-apps/usr/lib/seqan/bin/mason_methylation - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/tree_recon debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/tree_recon - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug debian/seqan-apps/usr/lib/seqan/bin/tree_recon - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/param_chooser debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/param_chooser - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug debian/seqan-apps/usr/lib/seqan/bin/param_chooser - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/pair_align debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/pair_align - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug debian/seqan-apps/usr/lib/seqan/bin/pair_align - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sgip debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sgip - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug debian/seqan-apps/usr/lib/seqan/bin/sgip - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/razers3 debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/razers3 - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug debian/seqan-apps/usr/lib/seqan/bin/razers3 - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/bam2roi debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/bam2roi - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug debian/seqan-apps/usr/lib/seqan/bin/bam2roi install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/a6 objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/a6/103a7d8b5eb8d6556a15aefb433ffee155269f.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/a6/103a7d8b5eb8d6556a15aefb433ffee155269f.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/a6/103a7d8b5eb8d6556a15aefb433ffee155269f.debug debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rep_sep debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rep_sep + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug debian/seqan-apps/usr/lib/seqan/bin/rep_sep + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/param_chooser debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/param_chooser + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/173367158657db07576d85b13012ef2ab8f4b0.debug debian/seqan-apps/usr/lib/seqan/bin/param_chooser + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_materializer debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_materializer + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug debian/seqan-apps/usr/lib/seqan/bin/mason_materializer + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/s4_search debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/s4_search + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug debian/seqan-apps/usr/lib/seqan/bin/s4_search install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_simulator debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/458efc5d3dd1cf3b8f17fa938c732055d4f604.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/458efc5d3dd1cf3b8f17fa938c732055d4f604.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_simulator objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/458efc5d3dd1cf3b8f17fa938c732055d4f604.debug debian/seqan-apps/usr/lib/seqan/bin/mason_simulator + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_variator debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_variator + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug debian/seqan-apps/usr/lib/seqan/bin/mason_variator + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_genome debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_genome + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug debian/seqan-apps/usr/lib/seqan/bin/mason_genome + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/gustaf debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/gustaf + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug debian/seqan-apps/usr/lib/seqan/bin/gustaf + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/3ceb659b5acce674c21cd2436999117b943fde.debug debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/bisar debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/bisar + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug debian/seqan-apps/usr/lib/seqan/bin/bisar + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/s4_join debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/s4_join + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/14/6b61268a323cbfe262bf12ef32dcd7d6455be1.debug debian/seqan-apps/usr/lib/seqan/bin/s4_join + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/fb objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/micro_razers debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/fb/4b348d6d306c6adc8775f0446748358d6c8715.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/fb/4b348d6d306c6adc8775f0446748358d6c8715.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/micro_razers objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/fb/4b348d6d306c6adc8775f0446748358d6c8715.debug debian/seqan-apps/usr/lib/seqan/bin/micro_razers - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/dfi debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/dfi - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug debian/seqan-apps/usr/lib/seqan/bin/dfi + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/60/b3192099feb26c60510ef9223e8cf18f54d935.debug debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/pair_align debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/pair_align + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/07/61acc2cd7a67aac544b254bb2e07f0516a9ce8.debug debian/seqan-apps/usr/lib/seqan/bin/pair_align install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c9 objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/alf debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c9/3acab2213daa62cdd634e72bfb5bab85308834.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c9/3acab2213daa62cdd634e72bfb5bab85308834.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/alf objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c9/3acab2213daa62cdd634e72bfb5bab85308834.debug debian/seqan-apps/usr/lib/seqan/bin/alf + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/dfi debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/dfi + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/50/ebaccbdde194a10b1535e3a220042818fe749d.debug debian/seqan-apps/usr/lib/seqan/bin/dfi + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/casbar debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/casbar + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug debian/seqan-apps/usr/lib/seqan/bin/casbar + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/tree_recon debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/tree_recon + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/af/cf1afa27a3c29147818995f8530651049dad16.debug debian/seqan-apps/usr/lib/seqan/bin/tree_recon + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/bam2roi debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/bam2roi + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cb/ca39255cd64181d8200f13a630e60068987c8f.debug debian/seqan-apps/usr/lib/seqan/bin/bam2roi + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_methylation debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_methylation + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/69/8c40bea608992ac19720b00d1333c7d4ffa37a.debug debian/seqan-apps/usr/lib/seqan/bin/mason_methylation + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/seqcons2 debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/seqcons2 + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6d/6cc97fdde90e5ae9905e005a056d1052a1e160.debug debian/seqan-apps/usr/lib/seqan/bin/seqcons2 install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/4e objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/samcat debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/4e/f58b02ea48bdabf8c8195dbd66e1b9df22ad36.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/4e/f58b02ea48bdabf8c8195dbd66e1b9df22ad36.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/samcat objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/4e/f58b02ea48bdabf8c8195dbd66e1b9df22ad36.debug debian/seqan-apps/usr/lib/seqan/bin/samcat - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rep_sep debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rep_sep - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/ff/a2a03ca6ee6fbdea448016116c0d4274ceb490.debug debian/seqan-apps/usr/lib/seqan/bin/rep_sep - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sak debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sak - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug debian/seqan-apps/usr/lib/seqan/bin/sak - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sam2matrix debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sam2matrix - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug debian/seqan-apps/usr/lib/seqan/bin/sam2matrix - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/s4_search debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/s4_search - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/833b48430ea2cc3100137d7231210c93bc8d95.debug debian/seqan-apps/usr/lib/seqan/bin/s4_search - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/cc/01e809e362214e4a11ac2224a9be21f817080e.debug debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/snp_store debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/snp_store + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug debian/seqan-apps/usr/lib/seqan/bin/snp_store objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/stellar debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/049a27722c462664fe14d4df30203d8fee1329.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/049a27722c462664fe14d4df30203d8fee1329.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/stellar objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/dd/049a27722c462664fe14d4df30203d8fee1329.debug debian/seqan-apps/usr/lib/seqan/bin/stellar - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_materializer debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_materializer - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6b/d31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d.debug debian/seqan-apps/usr/lib/seqan/bin/mason_materializer - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/insegt debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/insegt - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug debian/seqan-apps/usr/lib/seqan/bin/insegt - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/bisar debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/bisar - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/33/22890bfa242937777c2beef63c11674226166a.debug debian/seqan-apps/usr/lib/seqan/bin/bisar - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_genome debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_genome - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/6e/7c1cc764d466cbb0e5249522ff00558bfcb075.debug debian/seqan-apps/usr/lib/seqan/bin/mason_genome - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/c8/88578a8b131707d37ed75a8c84fc377c84ff79.debug debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64 objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/four2three debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/bf93af72dcb7d57af3748a3d56dd8cb435e071.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/bf93af72dcb7d57af3748a3d56dd8cb435e071.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/four2three objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/bf93af72dcb7d57af3748a3d56dd8cb435e071.debug debian/seqan-apps/usr/lib/seqan/bin/four2three - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/bd/bf401e757ff55c6e1ac407c40d396794b644e1.debug debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8a objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/razers debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8a/07ec15c00906412c0aaa40e1884cb06b2e918a.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8a/07ec15c00906412c0aaa40e1884cb06b2e918a.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/razers objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8a/07ec15c00906412c0aaa40e1884cb06b2e918a.debug debian/seqan-apps/usr/lib/seqan/bin/razers - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/snp_store debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/snp_store - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/2b/a31456e8a7706f22bdbf0a866d2ce08faa4b56.debug debian/seqan-apps/usr/lib/seqan/bin/snp_store - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_variator debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_variator - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/01/71bb2ce33cf4538f45062979ea30890fc10306.debug debian/seqan-apps/usr/lib/seqan/bin/mason_variator - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90 - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/gustaf debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/gustaf - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/90/87d318b4fd09497a2aabe86e39b691fcc6a628.debug debian/seqan-apps/usr/lib/seqan/bin/gustaf - install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b - objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/casbar debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug - chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug - strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/casbar - objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/9b/39f7557d566a22391f6f969d5afae58fac8ff9.debug debian/seqan-apps/usr/lib/seqan/bin/casbar + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sam2matrix debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sam2matrix + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/22/747be8a109ac6401692627d5ce6a4448b1e5b2.debug debian/seqan-apps/usr/lib/seqan/bin/sam2matrix + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/razers3 debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/razers3 + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/e3/2ca912e105b52186e68cd41fb89760f78ec24a.debug debian/seqan-apps/usr/lib/seqan/bin/razers3 objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/mason_splicing debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/898f0cdc973e1930f5ba50800634b12036ec12.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/898f0cdc973e1930f5ba50800634b12036ec12.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/mason_splicing objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/64/898f0cdc973e1930f5ba50800634b12036ec12.debug debian/seqan-apps/usr/lib/seqan/bin/mason_splicing + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sak debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sak + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/0f/dd41d48f3283af7f43c20cda4a94b3efeb5aee.debug debian/seqan-apps/usr/lib/seqan/bin/sak install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/f3 objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/f3/c7da011337541a046662438300fc59dbe08f7c.debug chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/f3/c7da011337541a046662438300fc59dbe08f7c.debug strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/f3/c7da011337541a046662438300fc59dbe08f7c.debug debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/93/d6a5c27f882db941569373a11aaf70d37c555a.debug debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8b/64036d3b5556a0f822152b555967be09a9ec31.debug debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87 + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/insegt debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/insegt + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/87/f59d292c2575b6e4fedbdd58844e341190e607.debug debian/seqan-apps/usr/lib/seqan/bin/insegt + install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d + objcopy --only-keep-debug --compress-debug-sections debian/seqan-apps/usr/lib/seqan/bin/sgip debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug + chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug + strip --remove-section=.comment --remove-section=.note debian/seqan-apps/usr/lib/seqan/bin/sgip + objcopy --add-gnu-debuglink debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.build-id/8d/22acf53157e6817ded0036039403c0c7fc62fb.debug debian/seqan-apps/usr/lib/seqan/bin/sgip install -d debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.dwz cp --reflink=auto -a debian/seqan-apps/usr/lib/debug/.dwz/i386-linux-gnu debian/.debhelper/seqan-apps/dbgsym-root/usr/lib/debug/.dwz rm -fr debian/seqan-apps/usr/lib/debug/.dwz @@ -120250,7 +120320,7 @@ rm -f debian/seqan-apps/DEBIAN/shlibs dh_shlibdeps -a install -d debian/seqan-apps/DEBIAN - dpkg-shlibdeps -Tdebian/seqan-apps.substvars debian/seqan-apps/usr/lib/seqan/bin/seqcons2 debian/seqan-apps/usr/lib/seqan/bin/s4_join debian/seqan-apps/usr/lib/seqan/bin/mason_methylation debian/seqan-apps/usr/lib/seqan/bin/tree_recon debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails debian/seqan-apps/usr/lib/seqan/bin/param_chooser debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection debian/seqan-apps/usr/lib/seqan/bin/pair_align debian/seqan-apps/usr/lib/seqan/bin/sgip debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate debian/seqan-apps/usr/lib/seqan/bin/razers3 debian/seqan-apps/usr/lib/seqan/bin/bam2roi debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage debian/seqan-apps/usr/lib/seqan/bin/mason_simulator debian/seqan-apps/usr/lib/seqan/bin/micro_razers debian/seqan-apps/usr/lib/seqan/bin/dfi debian/seqan-apps/usr/lib/seqan/bin/alf debian/seqan-apps/usr/lib/seqan/bin/samcat debian/seqan-apps/usr/lib/seqan/bin/rep_sep debian/seqan-apps/usr/lib/seqan/bin/sak debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining debian/seqan-apps/usr/lib/seqan/bin/sam2matrix debian/seqan-apps/usr/lib/seqan/bin/s4_search debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam debian/seqan-apps/usr/lib/seqan/bin/stellar debian/seqan-apps/usr/lib/seqan/bin/mason_materializer debian/seqan-apps/usr/lib/seqan/bin/insegt debian/seqan-apps/usr/lib/seqan/bin/bisar debian/seqan-apps/usr/lib/seqan/bin/mason_genome debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee debian/seqan-apps/usr/lib/seqan/bin/four2three debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing debian/seqan-apps/usr/lib/seqan/bin/razers debian/seqan-apps/usr/lib/seqan/bin/snp_store debian/seqan-apps/usr/lib/seqan/bin/mason_variator debian/seqan-apps/usr/lib/seqan/bin/gustaf debian/seqan-apps/usr/lib/seqan/bin/casbar debian/seqan-apps/usr/lib/seqan/bin/mason_splicing debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard + dpkg-shlibdeps -Tdebian/seqan-apps.substvars debian/seqan-apps/usr/lib/seqan/bin/fx_bam_coverage debian/seqan-apps/usr/lib/seqan/bin/rep_sep debian/seqan-apps/usr/lib/seqan/bin/param_chooser debian/seqan-apps/usr/lib/seqan/bin/mason_materializer debian/seqan-apps/usr/lib/seqan/bin/s4_search debian/seqan-apps/usr/lib/seqan/bin/mason_simulator debian/seqan-apps/usr/lib/seqan/bin/mason_variator debian/seqan-apps/usr/lib/seqan/bin/mason_genome debian/seqan-apps/usr/lib/seqan/bin/gustaf debian/seqan-apps/usr/lib/seqan/bin/mason_frag_sequencing debian/seqan-apps/usr/lib/seqan/bin/rabema_evaluate debian/seqan-apps/usr/lib/seqan/bin/bisar debian/seqan-apps/usr/lib/seqan/bin/s4_join debian/seqan-apps/usr/lib/seqan/bin/rabema_prepare_sam debian/seqan-apps/usr/lib/seqan/bin/micro_razers debian/seqan-apps/usr/lib/seqan/bin/roi_feature_projection debian/seqan-apps/usr/lib/seqan/bin/pair_align debian/seqan-apps/usr/lib/seqan/bin/alf debian/seqan-apps/usr/lib/seqan/bin/dfi debian/seqan-apps/usr/lib/seqan/bin/casbar debian/seqan-apps/usr/lib/seqan/bin/tree_recon debian/seqan-apps/usr/lib/seqan/bin/bam2roi debian/seqan-apps/usr/lib/seqan/bin/mason_methylation debian/seqan-apps/usr/lib/seqan/bin/seqcons2 debian/seqan-apps/usr/lib/seqan/bin/samcat debian/seqan-apps/usr/lib/seqan/bin/snp_store debian/seqan-apps/usr/lib/seqan/bin/stellar debian/seqan-apps/usr/lib/seqan/bin/roi_plot_thumbnails debian/seqan-apps/usr/lib/seqan/bin/four2three debian/seqan-apps/usr/lib/seqan/bin/razers debian/seqan-apps/usr/lib/seqan/bin/sam2matrix debian/seqan-apps/usr/lib/seqan/bin/razers3 debian/seqan-apps/usr/lib/seqan/bin/mason_splicing debian/seqan-apps/usr/lib/seqan/bin/sak debian/seqan-apps/usr/lib/seqan/bin/rabema_build_gold_standard debian/seqan-apps/usr/lib/seqan/bin/seqan_tcoffee debian/seqan-apps/usr/lib/seqan/bin/gustaf_mate_joining debian/seqan-apps/usr/lib/seqan/bin/insegt debian/seqan-apps/usr/lib/seqan/bin/sgip dh_installdeb install -d debian/libseqan2-dev/DEBIAN dh_gencontrol @@ -120261,16 +120331,16 @@ echo misc:Pre-Depends= >> debian/seqan-apps.substvars install -d debian/.debhelper/seqan-apps/dbgsym-root/DEBIAN dpkg-gencontrol -pseqan-apps -ldebian/changelog -Tdebian/seqan-apps.substvars -Pdebian/.debhelper/seqan-apps/dbgsym-root -UPre-Depends -URecommends -USuggests -UEnhances -UProvides -UEssential -UConflicts -DPriority=optional -UHomepage -UImportant -UBuilt-Using -DAuto-Built-Package=debug-symbols -UProtected -DPackage=seqan-apps-dbgsym "-DDepends=seqan-apps (= \${binary:Version})" "-DDescription=debug symbols for seqan-apps" "-DBuild-Ids=0171bb2ce33cf4538f45062979ea30890fc10306 0761acc2cd7a67aac544b254bb2e07f0516a9ce8 0fdd41d48f3283af7f43c20cda4a94b3efeb5aee 146b61268a323cbfe262bf12ef32dcd7d6455be1 22747be8a109ac6401692627d5ce6a4448b1e5b2 2ba31456e8a7706f22bdbf0a866d2ce08faa4b56 3322890bfa242937777c2beef63c11674226166a 4ef58b02ea48bdabf8c8195dbd66e1b9df22ad36 50ebaccbdde194a10b1535e3a220042818fe749d 60b3192099feb26c60510ef9223e8cf18f54d935 64898f0cdc973e1930f5ba50800634b12036ec12 64bf93af72dcb7d57af3748a3d56dd8cb435e071 698c40bea608992ac19720b00d1333c7d4ffa37a 6bd31e6a0a3f3c26d73c3d6a981bdf1eed96cd0d 6d6cc97fdde90e5ae9905e005a056d1052a1e160 6e7c1cc764d466cbb0e5249522ff00558bfcb075 87f59d292c2575b6e4fedbdd58844e341190e607 8a07ec15c00906412c0aaa40e1884cb06b2e918a 8b64036d3b5556a0f822152b555967be09a9ec31 8d22acf53157e6817ded0036039403c0c7fc62fb 9087d318b4fd09497a2aabe86e39b691fcc6a628 93d6a5c27f882db941569373a11aaf70d37c555a 9b39f7557d566a22391f6f969d5afae58fac8ff9 a6103a7d8b5eb8d6556a15aefb433ffee155269f afcf1afa27a3c29147818995f8530651049dad16 bdbf401e757ff55c6e1ac407c40d396794b644e1 c8833b48430ea2cc3100137d7231210c93bc8d95 c888578a8b131707d37ed75a8c84fc377c84ff79 c93acab2213daa62cdd634e72bfb5bab85308834 cbca39255cd64181d8200f13a630e60068987c8f cc01e809e362214e4a11ac2224a9be21f817080e dd049a27722c462664fe14d4df30203d8fee1329 dd458efc5d3dd1cf3b8f17fa938c732055d4f604 e32ca912e105b52186e68cd41fb89760f78ec24a e33ceb659b5acce674c21cd2436999117b943fde f3c7da011337541a046662438300fc59dbe08f7c fb4b348d6d306c6adc8775f0446748358d6c8715 ff173367158657db07576d85b13012ef2ab8f4b0 ffa2a03ca6ee6fbdea448016116c0d4274ceb490" -DSection=debug -UMulti-Arch -UReplaces -UBreaks + chmod 0644 -- debian/libseqan2-dev/DEBIAN/control chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/DEBIAN/control dpkg-gencontrol -pseqan-apps -ldebian/changelog -Tdebian/seqan-apps.substvars -Pdebian/seqan-apps - chmod 0644 -- debian/libseqan2-dev/DEBIAN/control chmod 0644 -- debian/seqan-apps/DEBIAN/control dh_md5sums cd debian/seqan-apps >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums cd debian/libseqan2-dev >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums + chmod 0644 -- debian/libseqan2-dev/DEBIAN/md5sums chmod 0644 -- debian/seqan-apps/DEBIAN/md5sums cd debian/.debhelper/seqan-apps/dbgsym-root >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums - chmod 0644 -- debian/libseqan2-dev/DEBIAN/md5sums chmod 0644 -- debian/.debhelper/seqan-apps/dbgsym-root/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/seqan-apps .. @@ -120285,12 +120355,14 @@ dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/22548/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/22033 and its subdirectories -I: Current time: Fri May 21 07:00:07 -12 2021 -I: pbuilder-time-stamp: 1621623607 +I: removing directory /srv/workspace/pbuilder/22548 and its subdirectories +I: Current time: Fri Jun 24 15:44:04 +14 2022 +I: pbuilder-time-stamp: 1656035044